Contacts of the helix formed by residues 37 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLN* 3.0 27.8 + - + +
36A ILE* 1.3 74.8 - - - +
38A ASP* 1.3 61.7 + - - +
39A ASN* 2.8 22.9 + - - +
40A VAL* 2.9 14.3 + - - +
41A ALA* 2.8 28.4 + - - +
70A SER* 4.4 6.1 - - - -
73A ALA* 3.6 10.7 - - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 1.3 77.1 - - - +
39A ASN* 1.3 57.2 + - - +
41A ALA* 3.7 2.7 - - - +
42A ASN* 2.8 30.7 + - - +
70A SER* 4.4 5.2 + - - -
72A THR* 4.6 2.8 + - - -
73A ALA* 3.6 15.7 + - - +
33B GLY 3.2 18.6 - - - +
34B SER* 4.8 2.5 - - - -
65B ASN* 3.6 36.3 + - - +
66B SER 5.0 0.3 - - - -
67B PRO* 3.9 19.9 - - - +
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 2.8 16.1 + - - +
38A ASP* 1.3 71.6 - - - +
40A VAL* 1.3 68.7 + - + +
42A ASN* 3.1 7.3 + - - +
43A SER* 2.9 24.0 + - - -
21B TYR* 4.0 2.9 + - - -
33B GLY 4.5 6.6 - - - +
34B SER* 4.9 8.1 - - - -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 31.0 - - + -
34A SER* 3.4 21.1 - - - +
35A GLN* 3.5 21.8 - - - +
36A ILE* 4.5 6.1 - - + -
37A ASP* 2.9 19.7 + - - +
39A ASN* 1.3 75.7 - - + +
41A ALA* 1.3 59.4 + - - +
43A SER* 3.1 7.1 + - - -
44A ILE* 2.8 41.0 + - + +
77A ILE* 5.1 1.6 - - + -
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Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 5.1 0.6 - - + +
37A ASP 2.8 20.9 + - - +
38A ASP* 3.7 4.3 - - - +
40A VAL* 1.3 71.5 - - - +
42A ASN* 1.3 64.1 + - - +
43A SER 3.1 0.2 + - - -
44A ILE 3.1 0.3 + - - -
45A VAL* 2.9 31.1 + - - +
73A ALA* 3.5 33.9 - - + +
76A ALA* 4.5 4.9 - - + -
77A ILE* 4.0 17.9 - - + +
65B ASN* 4.5 8.5 - - - +
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Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP 2.8 20.3 + - - +
39A ASN* 3.5 7.2 - - - +
41A ALA* 1.3 76.2 - - - +
43A SER* 1.3 61.2 + - - +
45A VAL* 4.1 3.0 - - - +
46A SER* 3.0 28.6 + - - -
21B TYR* 3.3 25.1 + - - +
31B MET* 3.5 38.3 - - - +
32B LEU 4.3 2.4 + - - -
33B GLY* 3.7 27.9 + - - +
65B ASN* 5.5 3.3 - - - +
93B ILE* 5.3 5.8 - - - +
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Residues in contact with SER 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN 2.9 12.4 + - - -
40A VAL* 3.4 10.1 - - - -
42A ASN* 1.3 75.6 - - - +
44A ILE* 1.3 61.6 + - - +
46A SER* 3.2 4.5 + - - -
47A GLN* 2.9 48.7 + - - +
4B ILE* 3.5 26.8 + - - +
5B PRO* 3.7 6.6 - - - +
20B ILE* 4.7 1.7 - - - +
21B TYR* 3.2 15.7 + - - -
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Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.8 28.9 - - + -
31A MET 4.1 12.6 - - - +
32A LEU* 4.4 17.9 - - + -
40A VAL* 2.8 32.6 + - + +
41A ALA 3.8 2.9 - - - +
43A SER* 1.3 73.4 - - - +
45A VAL* 1.3 62.2 + - - +
47A GLN* 3.0 14.1 + - - +
48A LEU* 2.9 33.2 + - + +
62A LEU* 4.7 10.3 - - + -
77A ILE* 3.9 38.4 - - + -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA 2.9 26.3 + - - +
42A ASN* 4.1 2.7 - - - +
44A ILE* 1.3 71.1 - - - +
46A SER* 1.3 64.5 + - - +
48A LEU* 3.0 7.2 + - - +
49A LEU* 2.9 31.6 + - + +
76A ALA* 3.8 21.3 - - + +
77A ILE* 4.2 5.8 - - - +
80A THR* 3.7 37.5 - - + +
31B MET* 3.8 21.1 - - + -
63B TYR* 5.5 2.0 - - + -
93B ILE* 3.9 17.9 - - + -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN 3.0 19.9 + - - -
43A SER 3.2 4.2 + - - -
45A VAL* 1.3 79.8 - - - +
47A GLN* 1.3 62.5 + - - +
49A LEU* 3.4 2.8 + - - +
50A PHE* 3.0 25.1 + - - +
20B ILE* 4.0 15.3 - - - -
21B TYR* 3.3 21.7 - - - -
24B LEU* 3.6 19.2 - - - +
31B MET* 3.4 19.6 - - - +
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Residues in contact with GLN 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 6.2 0.2 - - - +
25A LEU* 3.9 22.7 - - + +
29A ILE 4.9 0.5 - - - +
30A ILE* 3.4 40.8 - - + +
31A MET 4.8 1.6 + - - +
43A SER* 2.9 43.7 + - - +
44A ILE* 3.4 18.1 - - - +
46A SER* 1.3 71.8 - - - +
48A LEU* 1.3 58.7 + - - +
50A PHE* 3.3 3.1 + - - +
51A LEU* 2.8 34.3 + - - +
4B ILE* 5.3 0.6 - - - +
5B PRO* 3.6 26.6 - - + +
20B ILE* 4.2 11.4 - - + -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.8 20.2 - - + -
44A ILE* 2.9 31.3 + - + +
45A VAL* 3.0 6.7 + - - +
47A GLN* 1.3 74.2 - - - +
49A LEU* 1.3 62.9 + - - +
51A LEU* 3.1 5.7 + - - +
52A GLN* 3.1 22.7 + - - +
60A ILE* 4.3 9.4 - - + -
62A LEU* 5.9 2.7 - - + -
77A ILE* 4.5 3.4 - - + +
80A THR* 3.8 26.7 - - + -
81A ILE* 3.8 25.4 - - + +
84A ILE* 4.1 24.7 - - + +
88A VAL* 4.2 19.7 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 2.9 34.4 + - + +
46A SER 3.9 3.1 - - - +
48A LEU* 1.3 72.7 - - - +
50A PHE* 1.3 62.4 + - - +
52A GLN* 3.3 14.2 + - - +
53A ALA* 3.1 23.6 + - - +
80A THR* 4.5 7.9 - - + -
83A HIS* 5.3 7.2 - - + +
84A ILE* 4.2 19.1 - - + -
24B LEU* 4.4 21.3 - - + -
29B ILE* 4.8 9.4 - - + -
31B MET* 4.8 2.0 - - - -
63B TYR* 3.7 47.6 - - + +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.3 12.1 - - + -
26A LYS* 6.2 0.9 - - - -
46A SER 3.0 17.4 + - - +
47A GLN 3.5 3.6 - - - +
49A LEU* 1.3 78.8 - - - +
51A LEU* 1.3 81.2 + - + +
53A ALA* 3.3 7.5 + - + +
54A GLN* 3.2 54.6 + - + +
7B VAL* 3.2 30.7 - - + -
20B ILE* 3.7 19.5 - - + -
23B ARG* 3.4 47.6 - - + -
24B LEU* 3.7 12.5 - - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.6 37.2 - - + +
28A ARG* 3.0 56.2 + - + +
30A ILE* 4.0 10.3 - - + -
47A GLN 2.8 17.1 + - - +
48A LEU 3.7 4.7 - - - +
50A PHE* 1.3 95.0 - - + +
52A GLN* 1.3 60.3 + - - +
54A GLN* 3.3 5.1 + - + +
55A ASP 3.1 11.4 + - - +
60A ILE* 3.8 39.9 - - + -
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 3.1 12.4 + - - +
49A LEU* 3.6 16.3 - - - +
51A LEU* 1.3 76.3 - - - +
53A ALA* 1.3 61.6 + - - +
54A GLN 3.1 0.9 - - - -
55A ASP 3.1 24.3 + - - -
56A SER* 3.4 13.9 + - - -
60A ILE* 4.9 0.8 - - - +
83A HIS* 4.6 5.4 + - - -
84A ILE* 3.3 23.6 - - + +
85A LYS* 2.8 43.0 - - - +
86A PRO* 3.9 18.6 - - + -
193B GLU* 5.0 2.4 + - - -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 3.1 11.3 + - - +
50A PHE* 3.7 11.4 - - + +
52A GLN* 1.3 79.1 - - - +
54A GLN* 1.3 62.3 + - + +
23B ARG* 5.4 6.5 + - - +
24B LEU* 6.4 0.4 - - + -
27B ASP* 4.2 18.4 - - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.2 7.6 - - - +
50A PHE* 3.2 45.5 + - + +
51A LEU* 3.4 11.2 - - + +
52A GLN 3.1 0.6 - - - -
53A ALA* 1.3 80.7 + - - +
55A ASP* 1.3 61.9 + - + +
7B VAL* 5.6 0.3 - - - +
9B GLU* 5.2 3.4 + - - -
23B ARG* 3.8 23.2 - - - +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.9 39.5 + - - +
51A LEU 3.1 3.8 - - - +
52A GLN* 3.1 5.4 + - - +
54A GLN* 1.3 82.4 - - + +
56A SER* 1.3 59.9 + - - +
57A GLU* 2.7 38.1 + - - +
58A LYS* 2.8 43.8 + - - +
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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