Contacts of the helix formed by residues 37 - 55 (chain B) in PDB entry 3V5I
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 ASP 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLN* 2.9 28.8 + - + +
36B ILE* 1.3 75.3 - - - +
38B ASP* 1.3 59.9 + - - +
39B ASN* 2.8 22.4 + - - +
40B VAL* 2.9 14.6 + - - +
41B ALA* 2.9 27.9 + - - +
70B SER* 4.5 6.1 - - - -
73B ALA* 3.6 10.5 - - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 1.3 76.0 - - - +
39B ASN* 1.3 57.8 + - - +
41B ALA* 3.8 2.8 - - - +
42B ASN* 2.9 30.3 + - - +
70B SER* 4.4 5.7 + - - -
72B THR* 4.6 3.3 + - - -
73B ALA* 3.5 19.7 + - - +
33C GLY 3.4 17.3 - - - +
34C SER* 5.2 1.9 - - - -
65C ASN* 3.6 32.0 + - - +
66C SER 5.1 0.3 - - - -
67C PRO* 4.1 18.5 - - - +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 2.8 16.7 + - - +
38B ASP* 1.3 71.6 - - - +
40B VAL* 1.3 66.8 + - + +
42B ASN* 3.2 6.4 + - - +
43B SER* 2.9 23.6 + - - -
21C TYR* 4.1 2.9 + - - -
33C GLY 4.4 7.8 - - - +
34C SER* 5.0 7.4 - - - -
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.7 29.8 - - + -
34B SER* 3.5 20.0 - - - +
35B GLN* 3.5 21.5 - - - +
36B ILE* 4.5 6.5 - - + -
37B ASP* 2.9 20.0 + - - +
39B ASN* 1.3 77.8 - - + +
41B ALA* 1.3 58.8 + - - +
43B SER* 3.0 7.8 + - - -
44B ILE* 2.8 41.9 + - + +
77B ILE* 5.1 1.6 - - + -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 5.0 0.4 - - + +
37B ASP 2.9 16.8 + - - +
38B ASP* 3.8 5.2 - - - +
40B VAL* 1.3 77.2 - - - +
42B ASN* 1.3 57.7 + - - +
44B ILE* 3.7 0.3 - - - +
45B VAL* 2.8 37.2 + - - +
73B ALA* 3.4 34.1 - - + +
76B ALA* 4.5 4.5 - - + -
77B ILE* 3.9 17.5 - - + +
65C ASN* 4.5 7.9 - - - +
93C ILE* 6.3 0.2 - - - -
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP 2.9 20.3 + - - +
39B ASN* 3.5 7.6 - - - +
40B VAL 3.2 0.2 - - - -
41B ALA* 1.3 75.6 - - - +
43B SER* 1.3 60.0 + - - +
45B VAL* 4.2 2.9 - - - +
46B SER* 3.0 28.9 + - - -
21C TYR* 3.3 26.3 + - - +
31C MET* 3.4 36.1 - - - +
32C LEU 4.5 2.2 + - - -
33C GLY* 3.8 29.0 + - - +
63C TYR* 5.8 0.2 - - - +
65C ASN* 5.3 4.5 - - - +
93C ILE* 4.9 8.0 - - - +
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 2.9 12.4 + - - -
40B VAL* 3.4 10.3 - - - -
42B ASN* 1.3 74.3 - - - +
44B ILE* 1.3 67.8 + - - +
46B SER* 3.2 4.9 + - - -
47B GLN* 2.9 42.5 + - - +
4C ILE* 3.7 25.4 + - - +
5C PRO* 3.9 5.9 - - - +
20C ILE* 4.8 1.5 - - - +
21C TYR* 3.4 16.8 + - - -
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.7 29.2 - - + -
31B MET 4.1 12.3 - - - +
32B LEU* 4.5 17.9 - - + -
40B VAL* 2.8 32.6 + - + +
41B ALA 3.8 2.7 - - - +
43B SER* 1.3 72.2 - - - +
45B VAL* 1.3 64.7 + - - +
47B GLN* 2.9 14.7 + - - +
48B LEU* 2.9 31.5 + - + +
62B LEU* 4.6 10.1 - - + -
77B ILE* 3.9 39.3 - - + -
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 2.8 25.3 + - - +
42B ASN* 4.2 3.4 - - - +
44B ILE* 1.3 70.2 - - - +
46B SER* 1.3 59.5 + - - +
48B LEU* 3.1 11.8 + - - +
49B LEU* 2.8 37.8 + - + +
76B ALA* 3.6 20.9 - - + +
77B ILE* 4.1 6.5 - - + +
80B THR* 3.4 31.2 - - + +
31C MET* 4.0 12.1 - - + -
63C TYR* 5.4 1.6 - - + -
93C ILE* 3.7 28.0 - - + -
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASN 3.0 20.9 + - - -
43B SER 3.2 4.5 + - - -
45B VAL* 1.3 77.5 - - - +
47B GLN* 1.3 57.7 + - - +
49B LEU* 4.5 1.3 - - - +
50B PHE* 3.0 30.3 + - - +
20C ILE* 4.0 15.0 - - - +
21C TYR* 3.5 20.0 - - - -
24C LEU* 3.6 21.2 - - - +
31C MET* 3.5 20.1 - - - +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.9 26.5 - - + +
29B ILE 4.9 0.3 - - - +
30B ILE* 3.6 40.6 - - + +
31B MET 4.9 2.2 + - - +
43B SER* 2.9 40.5 + - - +
44B ILE* 3.4 17.5 - - - +
46B SER* 1.3 74.7 - - - +
48B LEU* 1.3 60.2 + - - +
50B PHE* 3.3 5.7 + - - +
51B LEU* 2.9 34.7 + - - +
5C PRO* 3.9 21.6 - - + +
20C ILE* 4.4 7.9 - - + -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.7 20.0 - - + -
44B ILE* 2.9 30.9 + - + +
45B VAL* 3.4 7.2 - - - +
47B GLN* 1.3 76.1 - - - +
49B LEU* 1.3 63.3 + - - +
51B LEU* 3.2 6.1 + - - +
52B GLN* 3.1 22.7 + - - +
60B ILE* 4.3 9.2 - - + -
62B LEU* 5.9 3.1 - - + -
77B ILE* 4.5 2.9 - - + +
80B THR* 3.8 29.2 - - + -
81B ILE* 3.9 25.4 - - + +
84B ILE* 4.3 14.5 - - + +
88B VAL* 4.2 26.7 - - + -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 2.8 34.6 + - + +
46B SER 3.9 2.9 - - - +
48B LEU* 1.3 72.0 - - - +
50B PHE* 1.3 63.7 + - - +
52B GLN* 3.3 13.3 + - - +
53B ALA* 3.1 23.1 + - - +
80B THR* 4.5 8.3 - - + -
83B HIS* 5.3 7.9 - - + +
84B ILE* 4.2 19.5 - - + -
24C LEU* 4.6 18.2 - - + -
29C ILE* 5.0 8.1 - - + -
31C MET* 4.9 2.0 - - - -
63C TYR* 3.5 48.9 - - + +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.4 13.2 - - + -
26B LYS* 6.3 0.9 - - - -
46B SER 3.0 19.0 + - - +
47B GLN 3.5 4.9 - - - +
49B LEU* 1.3 78.6 - - - +
51B LEU* 1.3 79.2 + - + +
53B ALA* 3.3 8.5 + - + +
54B GLN* 3.1 54.7 + - + +
7C VAL* 3.5 27.6 - - + -
20C ILE* 3.9 16.2 - - + -
23C ARG* 3.6 45.1 - - + -
24C LEU* 3.7 16.1 - - + +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 3.6 36.6 - - + +
26B LYS 5.9 0.2 - - - -
28B ARG* 2.9 55.4 + - + +
30B ILE* 4.1 9.9 - - + -
47B GLN 2.9 17.4 + - - +
48B LEU 3.7 3.8 - - - +
50B PHE* 1.3 89.9 - - + +
52B GLN* 1.3 62.8 + - - +
54B GLN* 3.3 6.1 + - + +
55B ASP 3.2 10.7 + - - +
60B ILE* 3.8 42.0 - - + -
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Residues in contact with GLN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU 3.1 12.7 + - - +
49B LEU* 3.5 17.2 - - - +
51B LEU* 1.3 76.1 - - - +
53B ALA* 1.3 64.0 + - - +
54B GLN 3.0 1.5 + - - -
55B ASP* 3.1 23.9 + - - -
56B SER* 3.4 13.7 + - - -
60B ILE* 4.9 0.8 - - - +
83B HIS* 4.7 4.0 + - - -
84B ILE* 3.4 24.5 - - + +
85B LYS* 2.9 42.2 - - - +
86B PRO* 3.9 18.8 - - + -
193C GLU* 4.6 4.4 + - - -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU 3.1 11.2 + - - +
50B PHE* 3.3 11.9 + - + +
52B GLN* 1.3 78.7 + - - +
54B GLN* 1.3 64.5 + - + +
23C ARG* 5.6 4.9 - - - +
24C LEU* 6.4 0.4 - - + -
27C ASP* 4.4 16.8 - - - +
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 4.1 8.1 - - - +
50B PHE* 3.1 50.9 + - + +
51B LEU* 3.4 12.6 - - + +
52B GLN 3.0 0.4 - - - -
53B ALA* 1.3 82.1 + - - +
55B ASP* 1.3 61.9 + - + +
9C GLU* 5.3 2.8 + - - -
23C ARG* 3.9 16.4 - - - +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 2.8 41.5 + - - +
51B LEU 3.2 3.5 + - - +
52B GLN 3.1 3.6 + - - +
54B GLN* 1.3 83.0 - - + +
56B SER* 1.3 59.1 + - - +
57B GLU* 2.8 39.7 + - - +
58B LYS* 2.8 43.6 + - - +
86B PRO* 3.8 1.4 - - - +
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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) + - + + + + + -
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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