Contacts of the strand formed by residues 89 - 96 (chain E) in PDB entry 2VLK
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 ALA 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38E ARG* 3.6 30.1 - - + +
39E GLN 3.8 12.3 - - - +
40E ASP* 4.0 2.5 - - - +
87E PRO 3.1 3.6 + - - -
88E THR* 1.3 78.1 - - - +
90E PHE* 1.3 63.9 + - - +
91E TYR* 3.5 20.3 - - + -
110E ARG* 3.9 3.3 - - - -
111E LEU 3.0 31.8 + - - +
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Residues in contact with PHE 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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38D GLN* 4.0 2.9 - - - -
41D GLY* 3.6 27.1 - - - -
42D GLU 3.5 24.5 - - - -
38E ARG* 3.3 4.3 - - - -
39E GLN* 2.9 57.3 + - + +
89E ALA* 1.3 72.6 - - - +
91E TYR* 1.3 60.2 + - - +
92E LEU* 3.9 17.2 + - + +
107E PRO 3.5 19.1 - - - -
108E GLY* 3.8 7.9 - - - -
109E THR 3.4 27.1 - - - -
110E ARG* 3.5 31.2 - - + +
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Residues in contact with TYR 91 (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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8E GLN* 3.1 6.0 + - - -
23E LEU* 3.6 28.3 - - + -
36E TRP* 4.0 6.3 - - + -
37E TYR 3.3 11.2 - - - +
38E ARG* 3.9 8.1 + - + -
48E ILE* 3.9 14.1 - - + -
66E TYR* 2.9 41.9 + + - -
78E LEU* 4.0 13.9 - - + -
80E VAL* 4.3 4.7 - - + +
87E PRO* 2.8 32.8 + - - +
89E ALA* 3.5 24.5 - - + -
90E PHE* 1.3 72.7 - - - +
92E LEU* 1.3 60.5 + - - +
108E GLY* 3.1 2.6 - - - -
109E THR* 2.8 35.6 + - - +
111E LEU* 3.8 20.2 - - + -
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Residues in contact with LEU 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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38D GLN* 4.1 4.7 - - - +
43D GLY* 3.6 15.3 - - - +
44D PRO* 3.8 17.0 - - + -
8E GLN* 3.6 0.9 - - - +
36E TRP* 3.6 5.8 - - - -
37E TYR* 2.8 43.4 + - + +
38E ARG 6.4 0.4 - - - -
39E GLN* 4.3 2.9 - - + +
45E LEU* 3.7 26.9 - - + -
90E PHE* 3.9 25.7 + - + +
91E TYR* 1.3 77.3 - - - +
93E CYS* 1.3 59.7 + - - +
105E PHE* 4.3 12.6 - - + -
106E GLY 3.3 26.7 - - - +
107E PRO 4.1 0.4 - - - -
108E GLY* 3.7 14.6 - - - -
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Residues in contact with CYS 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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6E ILE* 4.7 0.4 - - - -
8E GLN* 2.8 19.3 + - + +
25E CYS* 2.0 54.1 - - + -
34E MET* 3.7 13.7 - - - -
35E TYR 3.3 13.5 - - - +
36E TRP* 4.1 14.4 - - + -
76E PHE* 5.1 1.1 - - - -
92E LEU* 1.3 74.9 - - - +
94E ALA* 1.3 67.1 + - - +
105E PHE* 3.4 4.6 - - - -
106E GLY 2.8 26.2 + - - +
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Residues in contact with ALA 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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6E ILE* 5.0 2.0 - - - -
34E MET* 3.4 3.8 - - - +
35E TYR* 3.0 31.7 + - + -
37E TYR* 4.2 4.9 - - + -
93E CYS* 1.3 79.7 - - - +
95E SER* 1.3 64.7 + - - +
103E GLN* 3.6 31.9 - - + +
104E TYR 3.1 13.9 - - - +
105E PHE* 3.8 18.6 - - + -
106E GLY 4.7 0.2 - - - +
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Residues in contact with SER 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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6E ILE* 4.3 3.6 - - - +
27E GLN* 4.2 11.9 - - - +
29E LEU* 3.9 13.5 - - - +
31E HIS* 2.9 27.5 + - - +
33E ALA 3.2 13.7 - - - -
34E MET* 3.9 13.7 - - - +
35E TYR* 4.4 1.1 - - - -
94E ALA* 1.3 78.2 - - - +
96E SER* 1.3 64.1 + - - +
103E GLN* 3.4 2.8 - - - -
104E TYR 2.9 32.1 + - - -
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Residues in contact with SER 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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31E HIS* 3.2 11.7 + - - +
33E ALA* 3.0 23.4 + - - +
35E TYR* 3.5 21.0 + - - -
95E SER* 1.3 76.3 - - - +
97E SER* 1.3 66.5 + - - +
98E ARG 2.9 21.9 + - - -
99E SER* 4.1 0.2 - - - -
101E TYR 3.8 10.9 + - - -
102E GLU 3.2 25.1 - - - -
103E GLN* 3.9 4.7 - - - -
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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