Contacts of the helix formed by residues 40 - 64 (chain A) in PDB entry 4NEF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 3.6 3.5 + - - -
39A PRO* 1.3 74.0 - - - +
41A VAL* 1.3 59.2 + - - +
42A LEU* 3.7 8.0 + - - +
43A GLN* 3.2 28.7 + - - +
44A ILE* 3.0 30.6 + - - +
42C LEU* 5.3 2.1 - - - +
43D GLN* 4.8 4.9 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 1.3 72.4 - - - +
42A LEU* 1.4 57.8 + - - +
44A ILE* 3.5 3.0 + - + -
45A ALA* 2.9 30.8 + - - +
173A LEU* 4.1 26.2 - - + +
176A ILE* 3.7 36.5 - - + +
177A HIS* 3.8 23.1 - - + +
37D ALA* 4.0 23.3 - - + +
43D GLN* 3.4 24.9 + - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 3.3 5.3 - - - +
41A VAL* 1.4 75.5 - - - +
43A GLN* 1.3 57.6 + - - +
45A ALA* 3.3 3.3 + - + +
46A MET* 2.9 42.8 + - - +
173A LEU* 3.8 20.2 - - + -
42C LEU* 3.7 22.7 - - + -
40D SER* 5.3 2.2 - - - +
42D LEU* 3.8 33.2 - - + -
43D GLN* 3.4 26.6 + - + +
46D MET* 3.7 33.7 - - + -
50D LEU* 6.0 0.2 - - + -
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 4.5 5.2 + - - -
37A ALA 5.6 0.4 + - - -
38A LEU 5.1 1.4 - - - +
39A PRO* 3.4 31.5 - - - +
40A SER* 3.2 25.5 + - - +
42A LEU* 1.3 77.9 - - - +
44A ILE* 1.4 57.6 + - - +
46A MET* 3.5 4.6 - - - +
47A ALA* 3.0 25.8 + - - +
40C SER* 4.8 4.3 - - - -
41C VAL* 3.3 41.5 + - - +
42C LEU* 3.5 31.2 + - + +
173C LEU* 4.0 15.4 + - + +
177C HIS* 4.4 6.5 + - - -
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 5.3 0.2 - - - +
30A SER 4.1 2.9 - - - +
31A ALA* 4.0 28.3 - - + +
39A PRO* 3.8 30.5 - - + +
40A SER 3.0 23.4 + - - +
41A VAL* 4.7 2.7 - - - +
43A GLN* 1.4 71.2 - - - +
45A ALA* 1.4 66.7 + - - +
47A ALA* 3.1 15.6 + - + +
48A PHE* 3.1 40.9 + - + -
172A HIS* 4.7 0.2 - - - +
176A ILE* 3.7 28.7 - - + -
180A GLY 5.8 1.1 - - - +
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL 2.9 18.4 + - - +
42A LEU* 3.5 6.5 - - + +
44A ILE* 1.4 74.6 - - - +
46A MET* 1.3 53.2 + - - +
48A PHE* 3.9 1.2 - - - +
49A GLY* 2.9 28.6 + - - -
169A ALA* 3.4 37.5 - - + +
172A HIS* 3.6 19.7 - - + -
173A LEU* 4.0 17.7 - - + +
176A ILE* 4.1 0.6 - - - +
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Residues in contact with MET 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 2.9 33.3 + - - +
43A GLN 3.5 6.1 - - - +
45A ALA* 1.3 75.4 - - - +
47A ALA* 1.3 56.9 + - - +
49A GLY* 4.5 0.9 - - - +
50A LEU* 2.8 60.4 + - + +
166A PHE* 3.7 31.0 - - + -
169A ALA* 4.9 9.6 - - - -
42C LEU* 3.6 28.0 - - + -
46C MET* 4.4 21.3 - - + -
166C PHE* 5.0 0.7 - - + -
173C LEU* 4.7 1.8 - - + -
46D MET* 4.5 16.2 - - + -
50D LEU* 5.4 1.1 - - - -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.8 3.1 - - - +
27A GLY* 4.9 5.1 + - - +
30A SER* 3.5 35.0 - - - +
43A GLN 3.0 13.8 + - - +
44A ILE* 3.1 10.3 + - - +
46A MET* 1.3 75.8 - - - +
48A PHE* 1.3 59.8 + - + +
51A GLY* 3.1 21.7 + - - -
170C LEU* 3.3 14.9 - - + +
173C LEU* 4.3 15.7 - - + +
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.6 31.2 - + + -
24A VAL* 6.0 0.7 - - - -
27A GLY* 3.3 40.6 - - - -
28A LEU* 3.9 4.0 - - + -
31A ALA* 4.2 4.3 - - + -
44A ILE* 3.1 44.2 + - + +
47A ALA* 1.3 73.6 - - + +
49A GLY* 1.3 60.6 - - - +
51A GLY* 3.3 1.5 + - - -
52A ILE 3.0 24.3 + - - -
168A VAL* 3.7 11.1 - - + +
172A HIS* 3.4 39.0 - + + +
180A GLY 5.7 1.1 - - - -
187A ARG* 3.7 47.1 - - + -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 2.9 18.9 + - - -
46A MET* 3.9 0.4 - - - -
48A PHE* 1.3 78.3 - - - +
50A LEU* 1.3 58.4 + - - +
51A GLY 3.2 0.5 + - - -
52A ILE* 3.3 0.7 + - - -
53A GLY 3.1 22.7 + - - -
165A GLY* 3.2 33.6 - - - -
166A PHE* 6.3 0.2 - - - -
168A VAL* 4.0 2.8 - - - +
169A ALA* 3.9 10.5 - - - -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 2.8 49.8 + - + +
49A GLY* 1.3 69.7 - - - -
51A GLY* 1.3 58.4 + - - +
53A GLY* 4.0 2.2 - - - +
54A THR* 2.6 37.4 + - - +
162A LEU* 5.7 2.5 - - + -
165A GLY* 5.5 0.9 - - - -
166A PHE* 4.4 11.9 - - + -
46C MET* 5.4 2.9 - - - -
166C PHE* 3.7 55.0 - - + +
169C ALA* 3.9 21.3 - - + -
170C LEU* 3.8 10.8 - - + +
173C LEU* 4.2 13.5 - - + -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 4.6 8.3 - - - -
26A PHE* 5.8 2.7 - - - -
47A ALA 3.1 19.0 + - - -
48A PHE 3.6 2.0 - - - -
49A GLY 3.1 0.4 - - - -
50A LEU* 1.3 77.3 - - - +
52A ILE* 1.4 62.0 + - - +
54A THR* 3.8 1.6 - - - -
55A LEU* 3.1 35.6 + - - +
170C LEU* 3.6 16.9 - - - +
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.5 40.8 - - + -
48A PHE 3.0 11.9 + - - +
49A GLY 4.0 1.8 - - - +
51A GLY* 1.4 70.7 - - - +
53A GLY* 1.3 61.1 + - - +
55A LEU* 3.2 3.7 + - - +
56A VAL* 2.8 42.3 + - + +
66A HIS 5.1 3.4 - - - +
67A ILE* 3.8 32.5 - - + +
68A ASN* 6.2 0.7 - - + -
141A LEU* 5.6 0.2 - - + -
145A ILE* 6.1 0.2 - - + -
164A ILE* 3.7 29.8 - - + -
165A GLY* 4.6 1.3 - - - -
168A VAL* 3.8 26.7 - - + -
184A ASN* 5.1 1.8 - - - +
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Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLY 3.1 14.8 + - - -
50A LEU* 4.1 2.7 - - - -
52A ILE* 1.3 77.7 - - - +
54A THR* 1.4 58.4 + - - +
56A VAL* 4.7 0.9 - - - -
57A GLN* 3.1 20.4 + - - +
161A ALA* 3.3 36.9 - - - +
162A LEU* 5.2 5.8 - - - -
165A GLY* 3.8 4.0 - - - -
163C SER* 5.7 0.2 + - - -
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 2.6 22.8 + - - -
51A GLY 3.8 3.6 - - - -
53A GLY* 1.4 73.8 - - - +
55A LEU* 1.3 61.7 + - + +
57A GLN* 3.3 7.2 + - - +
58A ALA* 2.9 27.9 + - + +
140C GLN* 3.4 30.5 - - + +
144C CYS* 3.9 15.4 - - + -
163C SER* 4.7 2.6 + - - -
166C PHE* 4.1 4.0 + - - +
167C SER* 3.7 31.7 + - - +
170C LEU* 3.8 7.9 - - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.4 26.9 - - + +
22A LEU* 3.9 31.2 - - + -
23A PHE* 3.6 26.0 - - + +
51A GLY* 3.1 21.6 + - - +
52A ILE 3.2 0.4 + - - +
54A THR* 1.3 78.8 - - + +
56A VAL* 1.3 55.2 + - - +
58A ALA* 4.4 4.9 - - + +
59A LEU* 2.8 52.9 + - + +
65A ALA* 3.9 3.1 - - - +
67A ILE* 3.6 19.1 - - + -
140C GLN* 5.4 7.2 - - + -
143C LEU* 6.0 1.8 - - + -
170C LEU* 6.0 1.8 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 2.8 40.5 + - + +
53A GLY 4.0 3.4 - - - +
55A LEU* 1.3 68.6 - - - +
57A GLN* 1.3 53.1 + - - +
60A GLY* 2.8 17.6 + - - -
64A GLY 5.4 2.2 - - - +
65A ALA* 3.6 30.7 - - + +
67A ILE* 4.3 2.2 - - + -
149A THR* 6.0 3.1 - - + -
160A PRO 5.3 0.2 - - - -
161A ALA* 3.9 18.4 - - + +
164A ILE* 3.9 30.1 - - + -
153C ARG* 2.6 31.7 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLY 3.1 19.1 + - - +
54A THR* 3.4 6.5 - - - +
56A VAL* 1.3 76.9 - - - +
58A ALA* 1.3 56.9 + - - +
158A GLY* 3.5 22.8 + - - +
161A ALA* 3.7 11.2 - - + +
144C CYS* 3.8 15.9 - - - +
147C ALA* 3.2 14.8 - - - +
148C SER* 2.9 37.9 + - - +
153C ARG* 2.6 38.5 + - - +
160C PRO* 3.6 13.5 - - - +
163C SER* 3.9 15.2 + - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 2.9 18.2 + - + +
55A LEU* 4.0 8.5 - - + +
57A GLN* 1.3 78.2 - - - +
59A LEU* 1.3 72.2 + - + +
61A HIS* 3.1 18.5 - - - -
62A ILE* 3.8 2.6 - - - +
140C GLN 5.2 0.7 - - - +
143C LEU* 3.8 34.8 - - + +
144C CYS* 3.9 5.8 - - + +
147C ALA* 3.5 12.4 - - - +
219C TYR* 4.2 4.2 - - - -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 3.7 14.1 - - + +
18A LEU* 4.7 10.3 - - + -
19A ALA* 3.6 34.5 - - + +
22A LEU* 5.5 0.7 - - + -
55A LEU* 2.8 31.5 + - + +
58A ALA* 1.3 89.4 - - + +
60A GLY* 1.3 57.4 + - - +
61A HIS* 3.3 3.4 - - - -
62A ILE* 2.9 31.7 + - + -
63A SER* 3.1 20.5 + - - +
65A ALA* 4.0 8.1 - - + -
143C LEU* 5.1 6.1 - - + -
219C TYR* 5.8 0.7 - - + -
223C LEU* 3.9 34.5 - - + -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 2.8 29.7 + - - -
59A LEU* 1.3 70.3 - - - +
61A HIS* 1.3 58.1 + - - +
64A GLY* 2.8 30.4 + - - -
65A ALA* 3.7 15.5 - - - +
153C ARG* 3.4 10.0 - - - +
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Residues in contact with HIS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 3.1 27.0 + - - -
60A GLY* 1.3 70.2 + - - -
62A ILE* 1.4 68.5 + - + +
147C ALA* 3.6 18.0 - - + +
152C ARG 4.5 3.8 - - - +
153C ARG* 3.5 50.5 + - - +
219C TYR* 2.8 23.4 + - - -
224C PHE* 3.2 40.7 - + + -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 4.8 1.9 - - - +
11A ARG* 3.8 27.1 - - + +
12A ALA* 3.6 12.5 + - - +
15A ALA* 3.8 10.8 - - + -
58A ALA 3.8 10.8 - - - +
59A LEU* 2.9 22.1 + - + +
61A HIS* 1.4 107.8 - - + +
63A SER* 1.3 55.6 + - - +
64A GLY 3.9 0.2 - - - -
85A ARG* 5.5 0.2 + - - -
219C TYR* 4.1 6.7 - - + -
223C LEU* 3.9 23.6 - - + +
224C PHE* 3.9 31.9 - - + -
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 3.2 27.4 - - - -
15A ALA* 3.8 12.3 - - - +
16A GLU* 3.0 20.4 + - - -
59A LEU* 3.1 8.7 + - - +
62A ILE* 1.3 77.0 - - - +
64A GLY* 1.3 59.2 + - - +
65A ALA* 3.3 8.0 + - - -
66A HIS* 3.6 5.0 + - - -
85A ARG* 5.4 0.2 - - - +
89A TYR* 2.9 36.9 + - - -
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 5.4 2.9 - - - +
60A GLY* 2.8 22.2 + - - -
63A SER* 1.3 76.6 - - - +
65A ALA* 1.4 68.7 + - - +
66A HIS* 3.5 11.3 + - - -
145A ILE* 6.0 2.3 - - - +
149A THR* 5.4 8.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il