Contacts of the helix formed by residues 42 - 62 (chain D) in PDB entry 2V32
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 THR 42 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C PRO* 3.9 17.7 - - + -
212C TYR* 3.6 4.3 - - - -
39D ARG* 2.8 36.1 + - + -
40D ASP 3.1 8.7 - - - +
41D PHE* 1.3 84.9 - - - +
43D PRO* 1.4 71.2 - - - +
44D VAL 3.8 0.2 - - - -
45D SER* 3.2 5.9 + - - -
46D THR* 2.6 32.4 + - - -
80D TRP* 4.2 0.6 - - - +
1221D BEZ 2.8 30.9 + - + -
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Residues in contact with PRO 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C MET* 3.7 31.9 - - + -
185C VAL 3.5 24.7 - - - +
187C PRO* 3.7 15.7 - - + -
212C TYR* 3.5 22.4 - - + +
213C LEU* 3.9 13.2 - - + +
214C ARG 4.3 1.8 - - - +
42D THR* 1.4 84.2 - - - +
44D VAL* 1.3 63.6 + - - +
46D THR* 3.2 13.7 + - - -
47D THR* 3.2 15.1 + - - +
1221D BEZ 3.0 21.1 - - - +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ALA* 3.7 22.0 - - + -
173C THR 3.5 28.0 - - - +
174C PRO* 4.0 4.9 - - + -
184C MET* 3.7 19.1 - - + -
43D PRO* 1.3 70.7 - - - +
45D SER* 1.3 61.4 + - - +
47D THR* 2.7 23.7 + - - -
48D GLU* 3.1 10.3 + - + +
128D ARG* 3.7 15.5 - - - +
147D ALA 4.9 0.4 - - - +
150D GLY* 3.7 20.2 - - - +
1221D BEZ 2.8 27.5 + - - +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D HIS* 3.6 15.3 - - - +
38D PRO* 3.8 3.3 - - - +
39D ARG 3.7 5.6 + - - -
42D THR* 3.2 14.9 + - - -
43D PRO 3.2 0.4 - - - -
44D VAL* 1.3 71.5 - - - +
46D THR* 1.3 61.3 + - - +
48D GLU* 3.5 3.5 + - - -
49D LEU* 3.0 35.0 + - - +
80D TRP* 3.7 20.4 - - - -
128D ARG* 3.0 24.0 + - - +
1221D BEZ 3.1 13.5 + - - -
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Residues in contact with THR 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 5.9 0.2 - - + -
212C TYR* 3.3 14.9 - - - +
213C LEU* 3.9 13.0 - - + -
42D THR 2.6 20.7 + - - -
43D PRO 3.2 8.0 + - - -
45D SER* 1.3 78.3 - - - +
47D THR* 1.3 57.1 + - - +
50D GLY* 2.9 27.9 + - - -
80D TRP* 2.9 23.6 + - - +
83D ASP* 4.3 2.7 - - + +
84D VAL* 4.0 25.4 - - - +
87D LEU* 3.5 22.1 - - + +
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Residues in contact with THR 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C PRO* 3.7 16.5 - - + +
175C ALA* 3.0 28.8 + - - +
184C MET* 4.4 14.6 - - + -
215C TYR* 4.7 7.9 - - + +
43D PRO 3.2 10.5 + - - +
44D VAL 2.7 19.3 + - - -
46D THR* 1.3 76.7 - - - +
48D GLU* 1.3 56.2 + - - +
50D GLY* 3.7 1.1 + - - -
51D ARG* 2.9 29.1 + - - +
87D LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ALA* 3.9 17.9 - - + -
37D HIS* 4.8 0.3 - - - +
44D VAL* 3.1 14.0 + - + +
45D SER* 3.8 5.5 - - - +
46D THR 3.3 0.2 - - - -
47D THR* 1.3 77.0 + - - +
49D LEU* 1.3 60.6 + - + +
51D ARG* 2.9 18.2 + - - +
52D VAL* 3.0 17.2 + - - +
128D ARG* 2.7 35.3 + - - -
150D GLY* 3.3 5.1 - - - -
151D ARG* 2.7 62.2 + - - +
153D PHE* 3.7 19.8 - - + -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PHE* 3.8 22.2 - - + -
37D HIS* 3.6 30.7 - - + +
45D SER 3.0 24.7 + - - +
48D GLU* 1.3 80.9 - - + +
50D GLY* 1.3 60.7 + - - +
52D VAL* 3.5 3.7 + - - -
53D ILE* 3.2 17.2 + - - +
68D ALA* 4.1 8.1 - - + -
80D TRP* 3.8 22.7 - - + -
84D VAL* 3.5 17.7 - - + -
94D MET* 5.2 0.2 - - + -
96D TYR* 2.6 44.0 + - + +
98D ILE* 3.9 14.8 - - + -
151D ARG* 5.0 0.7 - - - +
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D THR 2.9 18.0 + - - -
47D THR* 3.8 2.2 - - - -
49D LEU* 1.3 75.4 - - - +
51D ARG* 1.3 60.8 + - - +
53D ILE 3.4 2.1 + - - -
54D GLN* 3.3 20.7 + - - +
84D VAL* 3.4 14.1 - - - +
87D LEU* 5.1 2.2 - - - -
88D SER* 3.4 29.1 - - - -
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ALA* 4.3 6.1 - - + -
176C ASP* 3.3 26.4 + - - +
47D THR 2.9 18.5 + - - +
48D GLU* 2.9 9.0 + - - +
50D GLY* 1.3 72.2 - - - +
52D VAL* 1.3 60.9 + - - +
54D GLN* 2.9 41.9 + - - +
55D LEU* 3.0 67.5 + - + +
153D PHE* 4.1 13.2 - - + -
154D SER* 5.0 9.3 + - - +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D PHE* 4.1 20.6 - - + -
48D GLU 3.0 13.4 + - - +
49D LEU 3.8 7.6 - - - +
50D GLY 3.4 0.2 - - - -
51D ARG* 1.3 73.0 - - - +
53D ILE* 1.3 64.4 + - - +
55D LEU* 3.2 8.7 + - - +
56D GLU* 3.0 21.5 + - - +
59D PHE* 4.7 4.9 - - + -
66D LEU* 3.7 28.0 - - + -
96D TYR* 3.6 22.7 - - + +
153D PHE* 3.5 39.0 - - + -
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU 3.2 12.4 + - - +
50D GLY 3.4 7.0 - - - +
51D ARG 3.3 0.2 - - - -
52D VAL* 1.3 76.4 - - - +
54D GLN* 1.3 62.9 + - - +
56D GLU* 3.1 22.1 + - + +
84D VAL* 3.8 25.4 - - + -
85D LYS* 4.2 10.8 - - + -
88D SER* 3.6 27.6 - - - +
90D VAL* 3.8 25.0 - - + +
94D MET* 4.0 18.6 - - - -
95D PRO* 4.1 23.1 - - + -
96D TYR* 3.9 13.7 - - + +
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Residues in contact with GLN 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLY 3.3 10.4 + - - +
51D ARG* 2.9 45.4 + - - +
53D ILE* 1.3 77.9 - - - +
55D LEU* 1.3 61.6 + - - +
56D GLU* 3.4 0.7 + - - +
57D GLY 4.9 1.7 + - - -
58D ASP* 4.6 3.6 - - - +
87D LEU 4.1 4.2 + - - -
88D SER* 2.7 36.9 + - - +
90D VAL* 4.5 13.0 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D ARG* 3.0 55.2 + - + +
52D VAL* 3.2 4.2 + - - +
53D ILE 3.1 0.2 - - - -
54D GLN* 1.3 77.5 - - - +
56D GLU* 1.3 65.7 + - - +
57D GLY 3.2 2.2 - - - -
58D ASP* 3.1 24.0 + - + +
59D PHE* 3.0 37.7 + - + -
153D PHE* 3.7 32.5 - - + -
154D SER* 5.0 1.1 - - - +
157D LEU* 4.2 21.1 - - + -
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL 3.0 10.0 + - - +
53D ILE 3.1 18.0 + - - +
54D GLN 3.4 1.2 - - - +
55D LEU* 1.3 76.0 - - - +
57D GLY* 1.3 62.9 + - - +
59D PHE* 3.1 9.0 + - - +
60D LYS* 2.7 48.1 + - - +
66D LEU* 4.6 9.9 - - + +
95D PRO* 3.5 34.9 - - + +
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Residues in contact with GLY 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLN 4.9 2.0 + - - -
55D LEU 3.2 0.6 - - - -
56D GLU* 1.3 87.4 - - - +
58D ASP* 1.3 60.1 + - - +
60D LYS* 3.8 6.5 - - - +
61D LYS* 2.9 35.0 + - - +
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Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D GLN 4.6 3.1 - - - +
55D LEU* 3.1 31.6 + - - +
57D GLY* 1.3 75.0 - - - +
59D PHE* 1.3 60.8 + - - +
61D LYS* 3.3 18.6 + - - +
62D ARG* 3.2 40.9 + - - +
157D LEU* 3.8 19.7 - - + +
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.5 3.6 - - + -
52D VAL* 4.7 7.9 - - + -
55D LEU* 3.0 48.5 + - + -
56D GLU 3.5 4.7 - - - +
58D ASP* 1.3 73.7 - - - +
60D LYS* 1.3 66.1 + - - +
62D ARG* 3.1 7.6 + - - -
64D VAL* 3.0 54.2 + - + +
66D LEU* 3.7 42.2 - - + -
153D PHE* 4.9 13.0 - + + -
156D ILE* 4.2 16.6 - - + -
157D LEU* 3.9 22.4 - - + -
160D ILE* 3.6 26.9 - - + -
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLU* 2.7 34.0 + - - +
57D GLY* 3.9 9.2 - - - +
58D ASP 3.5 0.2 - - - -
59D PHE* 1.3 70.8 - - - +
61D LYS* 1.3 60.9 - - - +
63D GLY* 3.0 15.0 + - - +
64D VAL 4.3 5.5 + - - +
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Residues in contact with LYS 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLY 2.9 26.4 + - - +
58D ASP* 3.4 14.6 - - - +
59D PHE 3.2 0.2 - - - -
60D LYS* 1.3 73.2 - - - +
62D ARG* 1.3 67.0 + - + +
63D GLY 3.7 0.5 + - - -
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TRP* 4.9 1.0 - - - -
58D ASP* 3.2 44.8 + - - +
59D PHE* 3.1 7.5 + - - +
60D LYS 3.1 0.8 - - - -
61D LYS* 1.3 87.1 - - + +
63D GLY* 1.3 61.8 + - - +
64D VAL* 3.9 10.5 - - + -
157D LEU* 3.9 30.7 + - - +
160D ILE* 4.2 10.1 - - + -
161D ASP* 2.8 43.1 + - - +
164D GLN* 2.8 40.0 + - - +
179D PRO* 5.4 1.0 - - - +
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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) + - + + + + + -
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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