Contacts of the helix formed by residues 49 - 64 (chain D) in PDB entry 1V15
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 SER 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B LYS* 5.6 8.6 - - - +
5D ARG 4.3 5.6 - - - -
6D ASN* 4.4 12.6 - - - -
7D LYS 4.7 0.2 - - - -
47D PHE* 3.2 9.2 + - - +
48D LYS* 1.3 77.9 - - - +
50D PHE* 1.3 62.8 + - - +
51D ASP* 3.6 13.4 - - - +
52D ASP* 2.9 44.4 + - - +
53D PHE 3.4 4.2 + - - -
114D TYR* 3.2 13.9 + - - -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG* 3.3 40.4 + - + +
49D SER* 1.3 71.2 - - - +
51D ASP* 1.3 62.1 + - - +
52D ASP 3.1 0.2 - - - -
53D PHE* 3.0 26.7 + + - -
54D ARG* 2.8 41.0 + - + +
101D LEU* 3.7 42.4 - - + -
113D VAL* 3.7 39.9 - - + -
114D TYR* 3.1 15.5 + + - +
119D ILE* 4.0 6.3 - - + -
7K G 3.5 20.2 - - - -
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Residues in contact with ASP 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 5.8 1.8 - - - +
81B LYS* 4.5 13.4 - - + +
83B TYR* 5.0 4.7 + - - +
5D ARG 5.1 0.2 + - - -
6D ASN* 5.4 4.0 - - - +
49D SER* 3.6 11.9 + - - +
50D PHE* 1.3 78.2 - - - +
52D ASP* 1.3 62.4 + - - +
54D ARG* 2.6 43.4 + - - +
55D LYS* 3.3 22.3 + - - +
7K G 4.5 6.4 - - - +
8K C 3.4 25.1 + - + -
9L G 4.2 4.2 - - - +
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Residues in contact with ASP 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 3.3 29.2 + - - +
59B GLU* 5.2 3.1 - - - +
47D PHE* 4.2 5.1 - - + -
48D LYS* 3.2 50.8 + - - +
49D SER* 2.9 28.9 + - - +
50D PHE 3.1 0.4 - - - -
51D ASP* 1.3 75.9 - - - +
53D PHE* 1.3 64.4 + - - +
55D LYS* 3.4 8.8 - - - +
56D ALA* 3.0 22.9 + - - +
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Residues in contact with PHE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ALA* 3.9 21.3 - - + -
34D ILE* 5.6 2.5 - - + -
42D LEU* 4.3 8.1 - - + -
47D PHE* 3.7 28.2 - + + -
49D SER 3.4 8.8 + - - +
50D PHE* 3.0 31.9 + + - +
52D ASP* 1.3 77.5 - - - +
54D ARG* 1.3 67.1 + - - +
56D ALA* 2.8 6.9 + - - +
57D VAL* 2.8 41.4 + - + +
101D LEU* 4.4 5.4 - - + -
114D TYR* 4.1 22.9 - + + -
116D MET* 3.6 30.1 - - + -
119D ILE* 3.6 26.2 - - + -
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Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PHE* 2.8 27.3 + - + +
51D ASP* 2.6 42.9 + - - +
53D PHE* 1.3 73.6 - - - +
55D LYS* 1.3 61.6 + - - +
57D VAL* 3.0 13.2 + - - +
58D TRP* 3.0 35.7 + - + +
82D GLY 5.2 1.7 + - - +
84D SER* 5.2 0.7 - - - -
101D LEU* 4.0 24.0 - - + -
7K G 3.0 56.4 + - - -
8K C 2.7 42.8 + - - +
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASP* 5.1 11.7 - - - +
55B LYS* 5.2 20.0 - - + +
51D ASP 3.3 12.4 + - - +
52D ASP* 3.4 12.1 - - - +
53D PHE 3.2 0.2 - - - -
54D ARG* 1.3 78.0 - - - +
56D ALA* 1.3 57.0 + - - +
58D TRP 3.4 0.7 + - - -
59D GLU* 3.1 49.1 + - - +
81D LYS 3.9 10.5 + - - -
82D GLY* 3.3 37.1 + - - +
83D TYR* 4.0 22.6 - - - -
8K C 5.8 1.0 + - - -
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.0 15.5 - - + -
47D PHE* 3.8 22.2 - - + -
52D ASP 3.0 11.5 + - - +
53D PHE 2.8 11.7 + - - +
55D LYS* 1.3 70.8 - - - +
57D VAL* 1.3 60.1 + - - +
59D GLU* 4.0 7.9 - - - +
60D GLU* 3.0 35.5 + - - +
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TRP* 6.3 1.6 - - + -
34D ILE* 5.1 14.1 - - + -
35D PRO* 6.3 1.3 - - + -
38D ILE* 4.4 13.7 - - + +
42D LEU* 3.5 24.2 - - + -
53D PHE* 2.8 45.4 + - + +
54D ARG* 3.0 9.8 + - - +
56D ALA* 1.3 73.5 - - - +
58D TRP* 1.3 72.6 + - + +
60D GLU* 3.4 4.6 + - - +
61D VAL* 2.9 33.8 + - + +
101D LEU* 4.8 11.2 - - + -
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Residues in contact with TRP 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TRP* 4.3 12.3 - + - -
23D LEU* 4.3 9.9 - - + -
54D ARG* 3.0 41.2 + - + +
57D VAL* 1.3 82.3 - - + +
59D GLU* 1.3 60.1 + - - +
61D VAL* 3.4 38.2 + - + +
62D SER 3.0 19.9 + - - -
79D VAL* 3.0 23.4 - - + +
82D GLY* 4.0 10.5 - - - -
83D TYR 3.5 17.3 - - - +
84D SER* 3.5 39.2 + - - -
85D PRO* 3.6 26.5 - - + -
99D TYR* 3.8 15.8 + - + -
101D LEU* 4.6 14.5 - - + +
121D VAL* 3.9 23.6 - - + -
7K G 5.7 0.2 + - - -
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LYS* 5.2 13.0 - - - +
52B ASP* 5.3 5.8 - - - +
55D LYS* 3.1 45.1 + - - +
56D ALA* 4.1 6.7 - - - +
58D TRP* 1.3 75.1 - - - +
60D GLU* 1.3 60.9 + - + +
62D SER* 2.4 19.9 + - - +
63D LYS* 3.2 35.2 + - - +
79D VAL 3.3 14.6 + - - +
80D SER 4.1 9.0 - - - +
81D LYS 3.8 6.8 - - - +
82D GLY* 3.7 10.2 - - - +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.5 29.5 - - + +
41D LYS* 3.0 46.0 + - + +
42D LEU* 3.7 22.4 - - + +
56D ALA* 3.0 25.5 + - + +
57D VAL 3.6 3.8 - - - +
58D TRP 3.3 0.2 - - - -
59D GLU* 1.3 74.3 - - - +
61D VAL* 1.3 65.2 + - - +
63D LYS* 3.3 31.3 + - - +
64D ASP* 3.3 17.0 + - - +
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TRP* 4.2 20.6 - - + +
23D LEU* 6.0 0.9 - - + -
35D PRO* 5.9 0.2 - - + -
38D ILE* 3.6 16.4 - - + +
57D VAL* 2.9 23.2 + - + +
58D TRP* 3.4 43.1 - - + +
60D GLU* 1.3 76.7 - - - +
62D SER* 1.3 58.3 + - - +
64D ASP* 3.0 28.1 + - - +
67D LEU* 4.4 11.2 - - + +
68D SER* 3.7 6.0 + - - +
71D LEU* 4.5 11.9 - - + -
79D VAL* 4.1 13.7 - - + -
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Residues in contact with SER 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP 3.0 5.1 + - - -
59D GLU* 2.4 31.0 + - - +
61D VAL* 1.3 78.4 - - - +
63D LYS* 1.3 61.3 + - - +
64D ASP 3.3 1.0 + - - +
65D PRO* 4.7 0.9 - - - +
68D SER* 3.6 14.4 + - - -
76D LYS 4.7 0.2 - - - -
79D VAL* 3.4 14.6 - - - -
80D SER* 3.3 47.3 + - - -
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LYS* 6.1 3.2 - - - +
41D LYS* 5.4 8.3 - - - +
59D GLU* 3.2 37.2 + - - +
60D GLU* 3.3 34.8 + - - +
62D SER* 1.3 83.1 + - - +
64D ASP* 1.3 56.4 + - - +
65D PRO* 3.2 14.3 - - - +
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Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ARG* 2.8 35.6 + - - +
38D ILE* 4.8 1.7 - - + +
60D GLU 3.3 8.9 + - - +
61D VAL 3.0 8.9 + - - +
62D SER 4.2 0.4 - - - -
63D LYS* 1.3 74.4 - - - +
65D PRO* 1.3 59.1 - - - +
66D GLU* 3.0 31.9 + - - +
67D LEU* 3.2 34.9 + - + +
68D SER* 2.7 35.5 + - - -
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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