Contacts of the helix formed by residues 31 - 45 (chain O) in PDB entry 5A31
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 31 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O TRP* 3.6 27.3 + - + +
30O VAL* 1.3 77.9 - - - +
32O PRO* 1.3 78.6 - - - +
33O TYR 3.6 2.0 + - - -
34O LYS* 3.1 21.2 + - + +
35O ILE* 2.9 22.5 + - - +
72O ASP* 3.1 26.0 + - - +
154O LEU* 4.2 6.3 - - - -
206O PRO 5.7 5.2 - - - +
208O SER* 6.6 0.2 - - - -
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Residues in contact with PRO 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O THR* 1.3 89.3 - - - +
33O TYR* 1.3 59.1 + - - +
35O ILE* 2.8 30.6 - - + +
36O ALA 3.1 3.8 + - - -
154O LEU* 4.6 7.2 - - + +
157O ALA* 3.5 37.0 - - + +
158O LEU* 3.9 7.9 - - + +
161O TYR* 3.4 41.0 - - + -
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Residues in contact with TYR 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O THR* 3.3 1.4 + - - -
32O PRO* 1.3 79.0 - - - +
34O LYS* 1.3 70.5 + - + +
36O ALA* 3.0 3.5 + - - +
37O VAL* 2.9 49.4 + - + +
67O LEU* 3.2 48.8 + - - +
71O PRO 4.0 10.1 + - - -
72O ASP* 3.4 42.2 - - + +
73O ILE* 3.3 44.4 - - + +
78O LEU* 4.3 11.0 - - + -
161O TYR* 3.1 24.7 - - + +
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Residues in contact with LYS 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O ASP* 5.8 2.5 - - - -
29O TRP 4.9 2.5 - - - +
30O VAL* 4.9 0.9 - - - -
31O THR* 3.1 28.6 + - + +
33O TYR* 1.3 90.9 - - + +
35O ILE* 1.3 56.7 + - - +
37O VAL* 4.0 3.3 - - - +
38O LEU* 3.0 32.2 + - - +
67O LEU 5.0 0.2 + - - -
68O LEU 4.3 13.9 + - - -
70O GLY 4.4 3.2 + - - -
72O ASP* 2.7 29.8 + - - +
135O PHE* 3.7 24.6 - - + -
139O MET* 3.7 38.8 - - + -
208O SER* 5.7 3.4 - - - -
211O GLN* 3.2 18.1 - - - +
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Residues in contact with ILE 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O VAL* 4.4 6.2 - - + +
31O THR 2.9 10.7 + - - +
32O PRO* 2.8 29.8 - - + +
34O LYS* 1.3 76.8 - - - +
36O ALA* 1.3 58.3 + - - +
38O LEU* 3.3 6.6 + - + +
39O VAL* 3.0 27.6 + - - +
97O ILE* 5.7 1.3 - - + -
100O MET* 4.6 6.7 - - + +
108O MET* 4.7 5.4 - - + -
111O PHE* 3.7 23.6 - - + -
112O PHE* 3.1 44.9 - - + -
154O LEU* 5.2 4.5 - - + -
158O LEU* 3.5 39.7 - - + -
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Residues in contact with ALA 36 (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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32O PRO 3.7 4.0 - - - +
33O TYR 3.0 3.6 + - - +
35O ILE* 1.3 80.2 - - + +
37O VAL* 1.3 63.3 + - - +
39O VAL* 3.0 20.4 - - - +
40O LEU* 3.2 8.7 + - - +
75O VAL* 4.9 1.1 - - + -
78O LEU* 4.0 14.5 - - + +
93O VAL* 4.4 3.4 - - + +
97O ILE* 3.4 31.6 - - + -
161O TYR* 3.5 27.4 - - + +
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Residues in contact with VAL 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O TYR* 2.9 57.9 + - + +
34O LYS* 4.1 5.2 - - + +
36O ALA* 1.3 72.6 - - - +
38O LEU* 1.3 65.9 + - - +
40O LEU* 3.4 8.4 + - + +
41O LEU* 3.1 25.7 + - + +
67O LEU* 4.1 19.3 - - + -
68O LEU* 3.6 32.1 - - + +
78O LEU* 4.2 6.3 - - + -
135O PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 38 (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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30O VAL* 5.9 0.2 - - + -
34O LYS 3.0 20.3 + - - +
35O ILE* 3.3 8.7 - - + +
36O ALA 3.2 0.2 - - - -
37O VAL* 1.3 77.0 - - - +
39O VAL* 1.3 57.3 + - - +
41O LEU* 3.2 12.8 + - + +
42O SER* 3.0 26.2 + - - -
111O PHE* 4.1 8.5 - - + -
112O PHE* 3.9 16.2 - - + -
115O LEU* 3.3 43.1 - - + -
135O PHE* 3.9 15.0 - - + -
136O LEU* 4.0 20.4 - - + -
139O MET* 3.6 26.2 - - + -
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Residues in contact with VAL 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE 3.0 11.4 + - - +
36O ALA* 3.0 23.1 - - - +
38O LEU* 1.3 73.2 - - - +
40O LEU* 1.3 66.2 + - - +
42O SER 3.2 0.7 + - - -
43O GLU* 2.9 41.6 + - + +
93O VAL* 3.8 11.7 - - + -
96O ARG* 3.4 42.2 - - + +
97O ILE* 3.7 26.7 - - + +
100O MET* 4.5 6.1 - - + -
111O PHE* 3.7 17.0 - - + -
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Residues in contact with LEU 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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36O ALA 3.2 8.4 + - - +
37O VAL* 3.6 11.9 - - + +
38O LEU 3.3 0.2 - - - -
39O VAL* 1.3 81.1 - - - +
41O LEU* 1.3 63.2 + - + +
43O GLU* 3.9 2.9 - - - +
44O MET* 2.9 58.6 + - + +
60O LEU* 4.0 9.4 - - + -
63O GLN* 4.6 4.9 - - - +
64O LEU* 5.4 1.1 - - + -
67O LEU* 3.5 31.6 - - + -
78O LEU* 4.4 8.5 - - + -
82O ILE* 3.7 36.6 - - + -
89O LEU* 4.4 5.9 - - + +
93O VAL* 4.3 14.1 - - + -
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Residues in contact with LEU 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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310I TRP* 4.6 4.7 - - + -
37O VAL* 3.1 18.5 + - + +
38O LEU* 3.2 11.0 + - + +
40O LEU* 1.3 79.0 - - + +
42O SER* 1.3 65.0 + - - +
44O MET* 3.9 12.2 - - + +
45O SER* 3.2 26.3 + - - -
64O LEU* 3.8 31.4 - - + -
68O LEU* 4.3 17.7 - - + -
132O VAL* 4.0 26.9 - - + +
135O PHE* 4.0 31.4 - - + -
136O LEU* 5.6 5.2 - - + -
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Residues in contact with SER 42 (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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38O LEU 3.0 16.2 + - - -
39O VAL 3.8 1.3 - - - -
41O LEU* 1.3 79.6 - - - +
43O GLU* 1.3 77.7 + - - +
45O SER* 3.6 16.8 + - - +
46O ARG* 3.9 8.0 + - - +
96O ARG* 5.5 0.7 + - - -
111O PHE* 4.3 9.8 - - - -
114O ASP* 5.7 1.4 + - - +
115O LEU* 4.1 25.9 - - - +
136O LEU* 6.4 0.9 - - - -
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Residues in contact with GLU 43 (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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39O VAL* 2.9 31.7 + - + +
40O LEU* 4.0 3.4 - - - +
42O SER* 1.3 93.5 + - - +
44O MET* 1.3 68.2 + - - +
46O ARG* 3.4 37.0 + - - +
49O GLU* 3.7 11.6 - - - +
89O LEU* 5.6 3.5 - - + +
92O SER* 4.1 22.2 - - - +
93O VAL* 5.5 2.5 - - - +
96O ARG* 3.0 46.5 + - + +
111O PHE* 4.6 0.5 - - - -
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Residues in contact with MET 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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310I TRP* 3.7 37.2 - - + -
40O LEU* 2.9 25.2 + - + +
41O LEU* 3.9 11.4 - - + +
43O GLU* 1.3 79.9 - - - +
45O SER* 1.3 62.7 + - - +
46O ARG 2.9 7.6 + - - +
49O GLU* 5.7 0.2 - - - -
50O GLY 3.2 25.5 + - - +
51O ALA* 6.3 1.3 - - + -
57O ARG* 5.9 8.3 - - + -
60O LEU* 3.4 47.8 - - + -
61O ASN* 5.2 2.7 - - - +
64O LEU* 3.9 5.4 - - + -
89O LEU* 3.9 20.2 - - + +
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Residues in contact with SER 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310I TRP* 3.7 35.5 + - - -
41O LEU 3.2 16.0 + - - -
42O SER* 3.8 7.0 + - - +
43O GLU 3.4 0.6 - - - -
44O MET* 1.3 78.1 - - - +
46O ARG* 1.3 58.2 + - - +
47O THR 4.3 0.2 + - - -
125O GLU* 4.4 18.0 - - - +
126O VAL* 3.9 17.3 + - - +
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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