Contacts of the helix formed by residues 37 - 55 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F GLN* 3.0 27.1 + - + +
36F ILE* 1.3 74.6 - - - +
38F ASP* 1.3 56.1 + - - +
39F ASN* 3.0 12.9 + - - +
40F VAL* 2.9 21.0 + - - +
41F ALA* 2.7 30.8 + - - +
70F SER* 4.5 5.2 - - - -
73F ALA* 3.7 11.0 - - - -
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Residues in contact with ASP 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ASP* 1.3 74.8 - - - +
39F ASN* 1.3 59.2 + - - +
41F ALA* 3.8 2.7 - - - +
42F ASN* 2.8 32.0 + - - +
70F SER* 4.4 6.6 + - - -
72F THR* 4.7 3.3 + - - -
73F ALA* 3.6 18.9 + - - +
33G GLY 3.5 20.8 - - - +
34G SER* 5.2 1.6 - - - -
65G ASN* 3.8 24.5 + - - +
67G PRO* 4.2 19.9 - - - +
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Residues in contact with ASN 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ASP* 3.0 11.3 + - - +
38F ASP* 1.3 75.5 - - - +
40F VAL* 1.3 69.0 + - + +
42F ASN* 3.2 7.3 + - - +
43F SER* 2.9 24.1 + - - -
21G TYR* 4.2 2.3 + - - -
33G GLY 4.8 5.7 - - - +
34G SER* 5.2 6.8 - - - -
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 3.8 28.3 - - + -
34F SER* 3.5 20.0 - - - +
35F GLN* 3.5 17.7 - - - +
36F ILE* 4.5 6.5 - - + -
37F ASP* 2.9 23.7 + - - +
39F ASN* 1.3 76.8 - - + +
41F ALA* 1.3 65.9 + - - +
43F SER* 3.0 8.4 + - - -
44F ILE* 2.9 35.7 + - + +
77F ILE* 5.2 1.1 - - + -
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Residues in contact with ALA 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F ILE* 4.9 0.9 - - + +
37F ASP 2.7 19.3 + - - +
38F ASP* 3.9 4.0 - - - +
40F VAL* 1.3 72.7 - - - +
42F ASN* 1.3 54.4 + - - +
44F ILE* 3.2 0.3 + - - -
45F VAL* 2.7 39.8 + - - +
73F ALA* 3.3 36.1 - - + +
76F ALA* 4.5 8.7 - - + -
77F ILE* 3.9 18.8 - - + +
65G ASN* 4.7 3.4 - - - +
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Residues in contact with ASN 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ASP 2.8 23.9 + - - +
39F ASN* 3.2 6.9 + - - +
41F ALA* 1.3 73.0 - - - +
43F SER* 1.3 56.8 + - - +
45F VAL* 4.1 3.6 - - - +
46F SER* 3.0 31.4 + - - -
21G TYR* 3.2 28.5 + - - +
31G MET* 3.4 35.3 - - - +
32G LEU 4.7 1.4 - - - -
33G GLY* 3.8 28.3 + - - +
65G ASN* 5.4 5.9 - - - +
93G ILE* 5.1 6.0 - - - +
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Residues in contact with SER 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASN 2.9 11.8 + - - -
40F VAL* 3.4 10.8 - - - -
42F ASN* 1.3 74.6 - - - +
44F ILE* 1.3 61.3 + - - +
46F SER* 3.2 6.3 + - - -
47F GLN* 2.9 47.8 + - - +
4G ILE* 3.4 27.6 + - - +
5G PRO* 3.8 5.9 - - - +
20G ILE* 4.9 1.0 - - - +
21G TYR* 3.4 12.7 + - - -
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Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 3.6 28.7 - - + -
31F MET 4.2 12.1 - - - +
32F LEU* 4.5 15.7 - - + -
40F VAL* 2.9 34.3 + - + +
41F ALA 3.8 2.5 - - - +
43F SER* 1.3 69.8 - - - +
45F VAL* 1.3 68.0 + - - +
47F GLN* 3.1 13.6 + - - +
48F LEU* 2.9 31.8 + - + +
62F LEU* 4.6 10.3 - - + -
77F ILE* 3.9 39.7 - - + -
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Residues in contact with VAL 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F ALA 2.7 27.4 + - - +
42F ASN* 4.1 4.0 - - - +
44F ILE* 1.3 72.0 - - - +
46F SER* 1.3 63.6 + - - +
48F LEU* 2.9 12.7 + - - +
49F LEU* 2.9 31.2 + - + +
76F ALA* 3.7 22.4 - - + +
77F ILE* 4.2 7.2 - - - +
80F THR* 3.6 29.6 - - + +
31G MET* 4.0 11.9 - - + -
63G TYR* 5.5 1.6 - - + -
93G ILE* 3.9 26.2 - - + -
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Residues in contact with SER 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F ASN 3.0 18.0 + - - -
43F SER 3.4 4.9 - - - -
45F VAL* 1.3 79.9 - - - +
47F GLN* 1.3 62.8 + - - +
49F LEU* 3.4 3.2 + - - +
50F PHE* 3.0 25.1 + - - +
20G ILE* 4.0 17.5 - - - +
21G TYR* 3.3 24.5 - - - -
24G LEU* 3.7 18.8 - - - +
31G MET* 3.7 15.9 - - - +
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Residues in contact with GLN 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 3.8 27.2 - - + +
29F ILE 4.9 0.3 - - - +
30F ILE* 3.5 39.0 - - + +
31F MET 4.9 1.2 + - - -
43F SER* 2.9 42.0 + - - +
44F ILE* 3.1 17.6 + - - +
46F SER* 1.3 75.0 - - - +
48F LEU* 1.3 62.1 + - - +
50F PHE* 3.3 2.6 + - - +
51F LEU* 3.0 27.7 + - - +
4G ILE* 5.5 0.2 - - - +
5G PRO* 3.8 21.8 - - + +
20G ILE* 4.4 11.0 - - + -
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Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 3.8 20.6 - - + -
44F ILE* 2.9 28.4 + - + +
45F VAL* 2.9 9.7 + - - +
47F GLN* 1.3 75.1 - - - +
49F LEU* 1.3 62.5 + - - +
51F LEU* 3.2 6.0 + - - +
52F GLN* 3.1 22.2 + - - +
60F ILE* 4.3 7.9 - - + -
62F LEU* 5.9 3.1 - - + -
77F ILE* 4.5 4.0 - - + +
80F THR* 3.9 27.4 - - + -
81F ILE* 3.9 25.6 - - + +
84F ILE* 4.1 25.6 - - + +
88F VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 2.9 31.2 + - + +
46F SER 3.9 4.3 - - - +
48F LEU* 1.3 76.1 - - - +
50F PHE* 1.3 61.6 + - - +
52F GLN* 3.4 12.9 + - - +
53F ALA* 3.1 23.2 + - - +
80F THR* 4.4 8.3 - - + -
83F HIS* 5.3 7.2 - - + +
84F ILE* 4.2 19.5 - - + -
24G LEU* 4.6 20.4 - - + -
29G ILE* 5.0 8.3 - - + -
31G MET* 4.7 2.9 - - - -
63G TYR* 3.7 47.1 - - + +
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Residues in contact with PHE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 4.5 13.2 - - + -
26F LYS* 6.3 0.7 - - - -
46F SER 3.0 17.7 + - - +
47F GLN 3.6 3.8 - - - +
49F LEU* 1.3 76.8 - - - +
51F LEU* 1.3 83.4 + - + +
53F ALA* 3.1 8.8 + - + +
54F GLN* 3.0 62.6 + - + +
7G VAL* 3.4 38.4 - - + -
20G ILE* 3.7 19.3 - - + -
23G ARG* 3.6 35.2 - - + -
24G LEU* 3.9 12.3 - - + +
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Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 3.6 37.5 - - + +
28F ARG* 3.0 56.1 + - + +
30F ILE* 4.1 10.5 - - + -
47F GLN 3.0 15.9 + - - +
48F LEU 3.2 5.1 + - - +
50F PHE* 1.3 93.8 - - + +
52F GLN* 1.3 61.2 + - - +
54F GLN* 3.3 5.3 + - + +
55F ASP 3.2 10.7 + - - +
60F ILE* 3.8 40.8 - - + -
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Residues in contact with GLN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU 3.1 12.1 + - - +
49F LEU* 3.7 15.9 - - - +
50F PHE 3.2 0.2 - - - -
51F LEU* 1.3 72.7 - - - +
53F ALA* 1.3 66.4 + - - +
54F GLN 3.0 2.6 + - - -
55F ASP 3.1 22.6 + - - -
56F SER* 3.4 12.9 + - - -
60F ILE* 4.9 0.6 - - - +
83F HIS* 4.7 4.4 + - - -
84F ILE* 3.5 24.9 - - + +
85F LYS* 2.9 41.4 - - - +
86F PRO* 3.8 19.1 - - + -
193G GLU* 4.8 2.6 + - - -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F LEU 3.1 11.1 + - - +
50F PHE* 3.1 12.1 + - + +
52F GLN* 1.3 79.4 + - - +
54F GLN* 1.3 63.2 + - + +
23G ARG* 5.4 6.3 - - - +
24G LEU* 6.3 0.7 - - + -
27G ASP* 4.4 17.3 - - - +
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ARG* 4.2 7.9 - - - +
50F PHE* 3.0 56.2 + - + +
51F LEU* 3.4 10.5 - - + +
52F GLN 3.0 0.6 - - - -
53F ALA* 1.3 82.1 + - - +
55F ASP* 1.3 62.0 + - + +
9G GLU* 5.2 3.4 + - - -
23G ARG* 3.9 16.8 - - - +
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Residues in contact with ASP 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ARG* 3.0 39.6 + - - +
51F LEU 3.2 4.1 + - - +
52F GLN 3.1 4.4 + - - +
54F GLN* 1.3 84.6 - - + +
56F SER* 1.3 59.7 + - - +
57F GLU* 2.8 39.4 + - - +
58F LYS* 2.9 44.1 + - - +
86F PRO* 3.9 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
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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