Contacts of the helix formed by residues 37 - 51 (chain A) in PDB entry 1V9P
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 TYR 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.8 42.6 - - + +
20A HIS* 4.4 9.9 - - + -
21A ASN* 3.6 30.2 + - + +
24A TYR* 6.4 1.1 - + + -
25A TYR* 4.7 17.9 - + - -
32A ILE* 3.6 23.6 - - + -
33A SER 3.0 21.8 + - - +
34A ASP* 4.0 14.4 - - - +
36A GLU* 1.3 75.7 - - - +
38A ASP* 1.3 77.5 + - - +
39A ARG 3.0 4.9 - - - -
40A LEU* 3.2 16.9 + - + +
41A LEU* 3.3 23.6 + - + +
65A GLY 5.2 7.1 + - - -
69A LEU* 4.8 1.6 - - - +
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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
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34A ASP* 2.8 27.9 - - - +
35A ALA* 2.9 10.7 + - - +
37A TYR* 1.3 84.2 - - - +
39A ARG* 1.3 56.1 + - - +
40A LEU 3.0 6.5 - - - -
41A LEU* 3.7 20.8 - - + +
42A ARG* 3.1 41.2 + - - +
65A GLY 5.8 1.6 - - - +
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Residues in contact with ARG 39 (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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35A ALA 3.3 11.6 + - - +
36A GLU* 3.1 26.7 - - + +
37A TYR 3.0 0.8 - - - -
38A ASP* 1.3 78.3 - - - +
40A LEU* 1.3 63.1 + - + +
42A ARG* 4.0 44.1 - - - +
43A GLU* 4.1 19.0 - - - +
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Residues in contact with LEU 40 (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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9A ARG* 4.9 6.5 - - - +
13A LEU* 3.6 26.1 - - + +
16A LEU* 4.4 32.1 - - + -
17A ILE* 3.6 13.2 - - + -
20A HIS* 5.9 1.1 - - + +
32A ILE* 5.0 14.6 - - + -
36A GLU* 2.9 44.2 - - - +
37A TYR* 3.2 9.6 + - + +
38A ASP 3.0 0.2 - - - -
39A ARG* 1.3 85.6 - - + +
41A LEU* 1.3 57.1 + - - +
42A ARG 3.0 4.9 - - - -
43A GLU* 3.3 2.4 + - - +
44A LEU* 3.0 29.6 + - - +
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Residues in contact with LEU 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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17A ILE* 3.3 25.0 - - + +
37A TYR* 3.3 24.6 + - + +
38A ASP* 3.4 28.9 + - + +
40A LEU* 1.3 80.6 - - - +
42A ARG* 1.3 59.8 + - - +
44A LEU* 3.7 8.5 - - - +
45A LYS* 3.7 8.3 + - - +
60A PRO* 4.5 3.8 - - + -
61A THR* 4.0 17.0 - - + +
64A VAL* 3.1 42.2 - - + -
65A GLY 4.9 7.4 - - - +
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Residues in contact with ARG 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* 3.1 24.8 + - - +
39A ARG* 4.0 38.4 - - - +
40A LEU 3.0 0.6 - - - -
41A LEU* 1.3 75.8 - - - +
43A GLU* 1.3 57.1 + - - +
44A LEU 3.0 1.3 - - - -
45A LYS* 2.7 31.1 + - + +
46A GLU* 2.9 11.2 + - + +
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Residues in contact with GLU 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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9A ARG* 2.6 50.9 + - - +
13A LEU* 3.6 9.5 - - + +
39A ARG* 4.1 21.9 + - - +
40A LEU* 3.3 7.7 + - - +
42A ARG* 1.3 78.9 - - - +
44A LEU* 1.3 60.2 + - - +
46A GLU* 3.1 10.2 + - + +
47A LEU* 2.8 50.1 + - + +
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Residues in contact with LEU 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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10A ILE* 4.6 6.7 - - + +
13A LEU* 3.7 24.5 - - + -
14A ARG* 3.0 29.4 - - + +
17A ILE* 3.8 10.8 - - + -
40A LEU 3.0 17.5 + - - +
41A LEU* 3.7 6.7 - - + +
43A GLU* 1.3 76.3 - - - +
45A LYS* 1.3 58.1 + - - +
47A LEU* 3.6 1.8 + - - +
48A GLU* 2.8 57.0 + - + +
59A SER* 3.3 4.3 - - - +
60A PRO* 3.3 39.5 - - + -
61A THR* 3.7 9.9 - - + -
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Residues in contact with LYS 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 LEU 3.7 8.9 + - - +
42A ARG* 2.7 19.5 + - + +
44A LEU* 1.3 73.9 - - - +
46A GLU* 1.3 60.8 + - - +
48A GLU* 3.8 9.5 + - + +
49A GLU* 3.4 49.7 + - - +
55A LYS* 5.5 2.2 - - - +
61A THR* 4.2 23.5 + - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.9 10.2 + - + +
43A GLU* 3.1 14.5 + - + +
45A LYS* 1.3 78.1 - - - +
47A LEU* 1.3 80.1 + - - +
49A GLU* 3.5 4.5 + - - +
50A ARG* 2.9 63.8 + - - +
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Residues in contact with LEU 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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1A MET* 3.3 42.2 - - + -
6A ALA* 4.0 17.9 - - - +
9A ARG* 4.0 14.1 - - + -
10A ILE* 4.0 17.2 - - + +
13A LEU* 4.6 2.7 - - + -
43A GLU* 2.8 52.4 + - + +
44A LEU* 4.3 0.9 - - - +
46A GLU* 1.3 89.3 - - - +
48A GLU* 1.3 65.3 + - - +
49A GLU 3.1 0.7 - - - -
50A ARG* 3.6 7.0 - - - -
51A PHE* 3.1 34.6 + - + +
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Residues in contact with GLU 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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10A ILE* 4.3 7.9 - - + -
14A ARG* 3.1 29.9 + - - +
44A LEU* 2.8 34.4 + - + +
45A LYS* 3.9 8.6 - - + +
46A GLU 3.3 0.2 - - - -
47A LEU* 1.3 78.2 - - - +
49A GLU* 1.3 62.5 + - - +
51A PHE 3.5 5.1 - - - +
52A PRO* 3.2 23.0 - - - +
55A LYS* 3.3 29.9 - - + +
59A SER* 2.6 21.5 + - - -
61A THR* 3.1 28.9 + - - +
62A GLU* 4.4 4.5 - - - +
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Residues in contact with GLU 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 LYS* 3.4 42.8 + - - +
46A GLU* 4.1 3.8 - - - +
47A LEU 3.1 0.4 - - - -
48A GLU* 1.3 82.9 - - - +
50A ARG* 1.3 56.9 + - - +
51A PHE 3.2 4.9 - - - -
52A PRO* 3.3 18.4 - - + +
55A LYS* 2.8 41.3 + - - +
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Residues in contact with ARG 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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1A MET* 3.5 41.5 - - - +
46A GLU* 2.9 58.8 + - - +
47A LEU* 3.6 2.5 - - - +
49A GLU* 1.3 75.3 - - - +
51A PHE* 1.3 97.5 + - + +
52A PRO* 3.5 4.6 - - - +
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Residues in contact with PHE 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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1A MET* 3.5 41.3 - - + -
3A ARG* 4.4 15.9 - - + -
6A ALA* 3.7 26.0 - - + -
47A LEU* 3.1 26.7 + - + +
48A GLU 3.5 7.8 - - - +
50A ARG* 1.3 116.4 - - + +
52A PRO* 1.3 69.3 - - - +
53A GLU* 2.9 21.8 + - - +
54A PHE* 3.0 30.7 + + + +
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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