Contacts of the helix formed by residues 87 - 98 (chain E) in PDB entry 6VVT
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 LYS 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489D GLU* 3.0 16.1 + - - +
490D VAL* 2.8 32.5 + - - +
492D ALA* 2.9 26.4 + - + +
493D GLU* 4.0 24.7 - - + +
494D HIS* 4.3 13.0 - - - -
552D GLN* 5.7 4.7 - - - +
556D ARG* 5.9 0.4 - - - +
85E GLN 4.1 10.5 - - - +
86E GLU* 1.3 76.4 - - - +
88E PRO* 1.3 75.0 - - + +
89E LEU* 4.4 4.7 - - + +
90E SER* 2.8 21.7 + - - +
91E ILE* 3.0 10.5 + - - +
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Residues in contact with PRO 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ALA* 4.0 19.1 - - + +
61E ILE* 3.9 24.5 - - + +
62E ASN* 3.9 27.1 - - + +
65E TYR* 6.1 5.2 - - + -
86E GLU 3.8 3.3 - - - +
87E LYS* 1.3 87.1 - - + +
89E LEU* 1.3 62.1 + - + +
91E ILE* 3.1 15.4 + - + +
92E ALA* 3.0 22.7 + - - +
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D ALA* 4.3 21.8 - - + +
552D GLN* 4.4 17.5 - - + +
553D ALA* 4.4 15.5 - - + +
556D ARG* 3.6 36.8 - - + +
54E ALA* 3.8 25.6 - - + +
55E ALA 4.4 0.2 - - - +
58E ALA* 3.7 23.4 - - + +
87E LYS* 3.2 4.8 - - + +
88E PRO* 1.3 80.9 - - + +
90E SER* 1.3 62.3 + - - +
92E ALA* 3.3 1.4 + - - +
93E LEU* 3.3 30.2 + - + +
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Residues in contact with SER 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D GLU* 3.3 32.9 + - - -
556D ARG* 3.5 25.0 + - - +
34E ASN* 5.1 4.2 + - - -
35E PRO* 5.7 0.3 - - - +
86E GLU* 3.6 17.1 - - - +
87E LYS* 2.8 17.4 + - - +
89E LEU* 1.3 78.8 - - - +
91E ILE* 1.3 59.2 + - - +
93E LEU* 3.7 5.8 + - - +
94E ARG* 3.5 22.0 + - - +
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Residues in contact with ILE 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ILE* 3.4 22.0 - - + -
65E TYR* 4.4 13.2 - - + +
78E PRO* 4.0 14.1 - - + -
80E VAL* 5.2 7.2 - - + +
82E PRO* 4.0 26.7 - - + -
86E GLU* 2.9 35.9 - - + +
87E LYS 3.0 12.6 + - - +
88E PRO* 3.1 13.9 + - + +
90E SER* 1.3 74.3 - - - +
92E ALA* 1.3 65.6 + - - +
93E LEU 3.1 1.8 - - - -
94E ARG* 3.1 7.1 + - - +
95E GLU* 3.0 34.5 + - + +
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA* 3.6 28.5 - - - +
57E ARG* 3.7 31.9 - - + +
58E ALA* 3.9 2.7 - - - +
61E ILE* 4.2 0.4 - - - +
88E PRO 3.0 14.7 + - - +
89E LEU 3.3 5.1 + - - +
91E ILE* 1.3 77.3 - - - +
93E LEU* 1.3 59.3 + - - +
95E GLU* 3.8 4.0 - - - +
96E ILE* 3.0 34.4 + - - +
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ALA* 6.4 0.2 - - + -
556D ARG* 3.4 47.3 - - + +
557D ILE* 4.6 13.2 - - + -
32E ILE 5.5 0.7 - - - +
34E ASN 5.0 0.4 - - - +
35E PRO* 4.0 19.2 - - + +
40E LEU* 3.5 27.4 - - + +
50E LEU* 4.5 10.8 - - + -
54E ALA* 3.6 23.8 - - + -
89E LEU* 3.3 22.9 + - + +
90E SER* 3.9 5.4 - - - +
91E ILE 3.1 0.8 - - - -
92E ALA* 1.3 75.2 - - - +
94E ARG* 1.3 61.0 + - - +
96E ILE* 3.3 3.4 + - + -
97E HIS* 3.0 23.7 + - - +
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Residues in contact with ARG 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ASN* 4.7 19.5 - - - +
35E PRO* 4.8 7.9 - - + -
80E VAL* 3.1 35.6 - - + +
81E GLU* 2.8 30.2 + - - +
82E PRO* 5.1 0.4 - - - -
83E GLY* 4.0 6.3 - - - +
86E GLU* 2.4 50.4 + - - -
90E SER* 3.5 8.4 + - - +
91E ILE* 3.1 10.1 + - - +
93E LEU* 1.3 77.9 - - - +
95E GLU* 1.3 62.4 + - - +
97E HIS* 3.1 9.9 + - + +
98E GLY* 3.1 18.5 + - - -
100E LEU* 4.8 0.2 - - - +
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ARG* 2.4 40.3 + - - -
61E ILE* 3.7 0.8 - - - +
78E PRO* 3.6 3.3 - - - +
79E LEU* 2.9 31.4 + - + +
80E VAL* 3.7 24.7 - - + +
91E ILE* 3.0 35.7 + - + +
92E ALA 3.8 3.8 - - - +
94E ARG* 1.3 76.4 - - - +
96E ILE* 1.3 61.2 + - - +
98E GLY 3.3 4.5 + - - -
100E LEU* 3.1 29.9 + - + +
101E LEU* 3.3 20.8 - - + +
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Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 4.1 11.4 - - + +
43E ARG* 3.2 36.3 - - + +
50E LEU* 4.2 11.0 - - + -
53E TYR* 3.6 41.7 - - + +
54E ALA* 3.7 27.4 - - + +
92E ALA* 3.0 18.0 + - + +
93E LEU* 3.7 5.4 - - - +
95E GLU* 1.3 77.0 - - - +
97E HIS* 1.3 62.3 + - - +
99E ASP* 3.2 10.5 + - - +
101E LEU* 4.2 22.0 - - + -
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Residues in contact with HIS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E PRO* 3.7 29.8 - - + +
36E PRO* 4.9 0.4 - - + +
39E GLU* 2.3 52.7 + - + +
40E LEU* 3.7 5.6 - - + +
43E ARG* 3.1 30.6 + - - +
93E LEU 3.0 13.6 + - - +
94E ARG* 3.1 11.1 + - + +
96E ILE* 1.3 77.9 - - - +
98E GLY* 1.3 58.5 + - - +
99E ASP* 3.7 0.2 - - - +
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Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E ARG 3.1 11.2 + - - -
95E GLU 3.3 0.2 + - - -
96E ILE 3.2 0.4 - - - -
97E HIS* 1.3 76.9 + - - +
99E ASP* 1.3 66.9 + - - +
100E LEU* 2.9 31.5 - - - +
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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