Contacts of the helix formed by residues 39 - 58 (chain O) in PDB entry 2D2C
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 VAL 39 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303N HEC 4.6 2.7 - - + -
35O ASP 3.9 6.7 - - - +
36O LEU* 3.1 51.4 - - + +
38O TYR* 1.3 85.8 - - - +
40O PHE* 1.3 56.3 + - + +
41O PRO* 3.1 1.4 - - - +
42O VAL* 2.4 23.8 + - + +
43O VAL* 2.4 43.0 + - + +
272P LEU 4.5 1.8 - - - +
273P ILE* 4.9 7.9 - - + -
276P LYS* 4.2 7.4 - - + -
23T GLN* 4.4 13.7 - - + -
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Residues in contact with PHE 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303N HEC 3.3 93.1 - + + -
1305N OPC 4.1 15.7 - - + -
36O LEU* 2.4 53.4 + - + +
37O LEU* 3.6 24.9 - - + -
39O VAL* 1.3 70.0 - - - +
41O PRO* 1.3 60.1 - - + +
43O VAL* 2.5 27.4 + - - +
44O ILE* 2.6 30.9 + - + +
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Residues in contact with PRO 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305N OPC 5.0 3.1 - - + -
37O LEU 2.7 31.2 - - - +
38O TYR* 3.1 9.6 - - - -
39O VAL 3.2 0.9 - - - +
40O PHE* 1.3 89.5 - - + +
42O VAL* 1.3 57.3 + - - -
44O ILE* 3.7 17.3 - - + -
45O MET* 2.8 38.4 + - + +
272P LEU* 3.1 29.6 - - + -
24Q PHE* 5.0 3.4 - - + -
27Q VAL* 5.2 5.2 - - + -
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Residues in contact with VAL 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O VAL* 2.4 38.5 + - + +
41O PRO* 1.3 68.8 - - - +
43O VAL* 1.3 65.7 + - - +
45O MET* 3.4 7.2 - - - -
46O GLY 3.2 10.4 + - - -
269P GLN* 3.1 31.8 - - + +
272P LEU* 3.0 35.0 - - + -
273P ILE* 3.7 8.1 - - + -
19T ALA* 3.7 14.4 - - - +
22T GLN* 3.5 22.2 - - + -
23T GLN* 3.9 5.8 - - + -
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Residues in contact with VAL 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N ILE* 3.2 33.9 - - + -
303N HEC 3.5 28.0 - - + -
39O VAL 2.4 30.6 + - - +
40O PHE* 2.5 21.3 + - + +
42O VAL* 1.3 62.2 - - - +
44O ILE* 1.3 58.0 + - - +
46O GLY* 2.5 31.7 + - - -
47O THR* 2.6 12.7 + - - -
1101R BCR 3.4 17.3 - - + -
23T GLN* 2.5 33.0 - - - +
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N THR* 4.4 16.0 - - + +
303N HEC 3.3 44.2 - - + -
1305N OPC 4.2 32.3 - - + +
40O PHE* 2.6 24.8 + - + +
41O PRO* 3.7 17.5 - - + +
43O VAL* 1.3 72.2 - - - +
45O MET* 1.3 60.6 + - + +
47O THR* 2.7 29.2 + - - -
48O PHE* 2.9 14.4 + - + +
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Residues in contact with MET 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O PRO* 2.8 32.1 + - + +
42O VAL* 3.4 3.1 - - - +
43O VAL 2.8 2.4 + - - -
44O ILE* 1.3 79.9 - - + +
46O GLY* 1.3 55.7 + - - +
48O PHE* 2.6 37.4 + - - +
49O ALA* 3.1 7.8 + - - +
265P VAL* 4.0 17.2 - - + +
268P ALA* 3.8 19.3 - - - -
269P GLN* 3.1 44.2 - - + +
272P LEU* 4.0 5.4 - - + -
27Q VAL* 4.4 16.4 - - + -
30Q VAL* 4.4 17.9 - - + -
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Residues in contact with GLY 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL 3.2 3.4 + - - -
43O VAL 2.5 12.3 + - - -
45O MET* 1.3 77.2 - - - +
47O THR* 1.3 55.4 + - - -
48O PHE 3.1 3.2 + - - -
49O ALA* 4.2 8.1 - - - +
50O CYS* 4.0 16.6 - - - -
265P VAL* 4.1 9.8 - - - +
1101R BCR 3.8 11.8 - - - +
16T LEU* 4.7 4.9 - - - +
19T ALA* 3.1 27.9 - - - +
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Residues in contact with THR 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N ILE* 3.8 33.8 - - + +
42N THR* 5.1 8.1 - - + +
43N CYS* 5.3 7.6 - - - -
46N ILE* 4.7 5.8 - - - +
96N MET* 4.2 8.7 - - + -
43O VAL* 2.6 36.0 + - - +
44O ILE* 2.7 11.1 + - - -
46O GLY* 1.3 72.4 - - - +
48O PHE* 1.3 58.1 + - - +
50O CYS* 5.0 2.5 - - - -
51O ILE* 3.4 17.3 - - - +
1101R BCR 3.8 24.1 - - + +
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Residues in contact with PHE 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N THR* 6.3 0.2 - - + -
46N ILE* 4.8 20.4 - - + -
85N ILE* 4.2 19.7 - - + -
1305N OPC 4.6 28.7 - - - -
44O ILE* 2.9 9.4 + - + +
45O MET* 2.6 22.3 + - - +
47O THR* 1.3 72.0 - - - +
49O ALA* 1.3 55.5 + - - +
50O CYS 2.5 18.8 + - - -
51O ILE* 2.7 26.5 + - + +
52O VAL* 3.5 28.7 - - + -
261P PHE* 4.9 11.9 - + - -
30Q VAL* 6.1 2.0 - - + -
34Q ALA* 3.8 29.2 - - + -
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Residues in contact with ALA 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O MET 3.1 9.2 + - - +
46O GLY* 4.2 8.1 - - - +
48O PHE* 1.3 81.0 - - - +
50O CYS* 1.3 51.0 + - - +
52O VAL* 2.8 15.4 + - - +
53O ALA* 2.7 33.7 + - + +
261P PHE* 5.8 7.2 - - + -
262P ILE* 5.5 7.6 - - + -
265P VAL* 4.8 15.4 - - + +
16T LEU* 4.2 26.9 - - + -
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Residues in contact with CYS 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92N MET* 5.5 5.2 - - + -
46O GLY 4.0 11.7 - - - -
47O THR* 5.5 0.9 - - - -
48O PHE 2.5 6.3 + - - +
49O ALA* 1.3 74.6 - - - +
51O ILE* 1.3 57.9 + - + +
52O VAL 2.7 3.1 + - - -
53O ALA* 2.9 9.1 + - - -
54O LEU* 2.4 52.2 + - + +
1101R BCR 4.8 8.5 - - - -
13T LEU* 3.6 21.8 - - + -
16T LEU* 3.7 16.6 - - - -
17T PHE* 4.3 17.5 - - - -
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Residues in contact with ILE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N CYS* 6.0 3.8 - - - -
46N ILE* 5.0 6.1 - - + -
85N ILE* 3.2 52.2 - - + +
88N TRP* 3.6 6.1 - - + -
89N SER* 3.4 25.4 - - - +
92N MET* 4.8 15.7 - - + -
47O THR 3.4 19.7 - - - +
48O PHE* 2.7 24.7 + - + +
50O CYS* 1.3 76.9 - - + +
52O VAL* 1.3 51.1 + - - +
54O LEU* 4.0 9.3 - - + +
55O SER* 2.5 40.6 + - - -
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Residues in contact with VAL 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N LEU* 5.0 7.2 - - + -
85N ILE* 4.4 9.9 - - + -
48O PHE* 3.5 33.7 - - + -
49O ALA* 2.8 12.7 + - - +
50O CYS 2.7 0.6 + - - -
51O ILE* 1.3 76.0 - - - +
53O ALA* 1.3 70.5 + - - +
54O LEU 2.9 0.6 + - - -
55O SER* 3.0 3.5 + - - -
56O VAL* 2.6 36.6 + - + +
258P MET* 3.9 34.1 - - + +
261P PHE* 5.9 10.1 - - + -
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Residues in contact with ALA 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O ALA* 2.7 16.1 + - + +
50O CYS* 3.3 6.1 - - - +
52O VAL* 1.3 71.2 - - - +
54O LEU* 1.3 51.8 + - - +
57O LEU* 2.5 45.9 + - - +
258P MET* 3.3 27.6 - - + -
262P ILE* 5.8 2.9 - - + -
12T THR 5.6 0.2 - - - -
13T LEU* 3.6 36.3 - - + -
16T LEU* 5.9 1.6 - - + -
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Residues in contact with LEU 54 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88N TRP* 3.6 48.5 - - + -
92N MET* 4.7 15.5 - - + -
50O CYS* 2.4 56.6 + - + +
51O ILE* 4.0 6.5 - - - +
53O ALA* 1.3 63.7 - - + +
55O SER* 1.3 54.4 + - - +
57O LEU* 4.2 2.9 - - - -
58O ASP* 2.4 45.0 + - + +
6R VAL* 5.3 12.1 - - + -
10T PHE* 5.6 10.3 - - + -
13T LEU* 4.5 18.6 - - + -
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Residues in contact with SER 55 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N TRP* 5.3 1.5 - - - -
81N LEU* 4.5 3.1 - - - -
84N SER* 2.8 24.7 + - - -
85N ILE* 2.6 33.0 + - - -
88N TRP* 3.6 5.5 - - - -
51O ILE 2.5 29.1 + - - -
52O VAL* 3.0 2.9 + - - -
54O LEU* 1.3 71.5 - - - +
56O VAL* 1.3 62.0 + - - +
58O ASP 2.5 28.2 - - - +
59O PRO* 2.9 12.1 - - - +
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Residues in contact with VAL 56 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N TRP* 3.4 19.3 - - + -
81N LEU* 3.2 32.8 - - + -
52O VAL* 2.6 39.5 + - + +
53O ALA 3.4 4.3 - - - +
55O SER* 1.3 70.8 - - - +
57O LEU* 1.3 62.9 + - + +
58O ASP* 4.4 0.2 - - - -
59O PRO* 5.7 0.2 - - - -
250P GLN* 2.7 38.1 + - - +
254P ARG* 4.6 7.2 - - - +
255P VAL* 5.4 2.4 - - + +
258P MET* 3.6 37.9 - - + -
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Residues in contact with LEU 57 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O ALA 2.5 34.2 + - - +
54O LEU* 3.7 2.7 - - - +
56O VAL* 1.3 75.2 - - + +
58O ASP* 1.3 59.2 + - - +
59O PRO* 4.1 2.1 - - - +
38P GLN* 3.1 24.9 + - - +
39P SER* 5.2 0.2 - - - -
248P VAL* 4.7 0.7 - - - +
250P GLN* 4.6 8.8 + - + +
255P VAL* 5.3 7.6 - - + -
258P MET* 3.9 8.5 - - + -
9T VAL* 2.8 44.6 - - + +
10T PHE* 3.3 49.8 - - + +
12T THR* 3.4 8.5 - - - +
13T LEU* 4.0 9.9 - - + -
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Residues in contact with ASP 58 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N ARG* 3.9 7.2 + - - -
88N TRP* 3.5 21.1 + - + -
54O LEU* 2.4 25.7 + - + +
55O SER* 2.5 19.4 - - - +
57O LEU* 1.3 75.1 - - + +
59O PRO* 1.3 87.3 - - - +
38P GLN* 4.6 8.7 + - - +
146P LYS* 3.1 25.7 + - - +
246P GLU* 5.4 1.6 - - - +
248P VAL* 4.8 2.9 - - - +
2R ILE* 4.7 12.8 - - + +
10T PHE* 5.1 8.1 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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