Contacts of the strand formed by residues 89 - 96 (chain J) in PDB entry 2VLR
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J ARG* 3.8 28.3 - - + +
39J GLN 4.2 6.1 - - - +
40J ASP* 4.1 6.7 - - - +
87J PRO 3.3 3.1 + - - +
88J THR* 1.3 78.6 - - - +
90J PHE* 1.3 63.0 + - - +
91J TYR* 3.6 24.7 - - + -
110J ARG* 3.9 5.0 + - - +
111J LEU 3.1 31.9 + - - +
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Residues in contact with PHE 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLN* 4.2 0.4 - - - -
41I GLY* 3.5 33.9 - - - -
42I GLU 3.7 22.4 - - - -
38J ARG* 3.4 3.8 - - - -
39J GLN* 2.8 68.0 + - + +
89J ALA* 1.3 72.9 - - - +
91J TYR* 1.3 59.5 + - - +
92J LEU* 3.8 21.9 + - + +
107J PRO 3.9 4.5 - - - -
108J GLY* 3.7 31.0 - - - -
109J THR 3.6 13.5 - - - -
110J ARG* 3.7 28.0 - - + +
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Residues in contact with TYR 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J GLN* 3.7 3.1 + - - -
23J LEU* 3.5 28.9 - - + -
36J TRP* 3.9 6.1 - + + -
37J TYR 3.7 11.4 - - - -
38J ARG* 3.8 13.2 + - + -
48J ILE* 3.9 8.7 - - + -
66J TYR* 2.7 38.6 + + - -
78J LEU* 3.9 17.5 - - + -
80J VAL* 4.6 5.9 - - + +
87J PRO* 2.8 29.9 + - - +
89J ALA* 3.6 26.4 - - + +
90J PHE* 1.3 72.2 - - - +
92J LEU* 1.3 61.3 + - - +
108J GLY* 3.3 7.1 - - - -
109J THR* 2.9 37.5 + - - +
111J LEU* 4.1 19.5 - - + -
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Residues in contact with LEU 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLN* 3.9 6.1 - - - +
43I GLY* 3.8 15.5 - - - -
44I PRO* 3.8 19.1 - - + -
8J GLN* 3.9 0.9 - - - -
36J TRP* 3.6 6.9 - - - -
37J TYR* 2.9 48.0 + - + +
38J ARG 6.3 0.2 - - - -
39J GLN* 4.2 3.4 - - + +
45J LEU* 3.7 27.4 - - + -
90J PHE* 3.8 34.0 + - + +
91J TYR* 1.3 71.0 - - - +
93J CYS* 1.3 58.1 + - - +
105J PHE* 4.2 13.9 - - + -
106J GLY 3.6 23.8 - - - +
108J GLY* 3.9 10.3 - - - -
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Residues in contact with CYS 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 4.4 2.5 - - + -
8J GLN* 3.2 18.9 + - + +
25J CYS* 2.0 52.9 - - + -
34J MET* 5.1 2.9 - - - -
35J TYR 3.3 14.1 - - - +
36J TRP* 4.1 16.4 - - + -
76J PHE* 4.9 7.9 - - - -
92J LEU* 1.3 74.2 - - - +
94J ALA* 1.3 75.0 + - - +
105J PHE* 3.5 4.9 - - - -
106J GLY 3.0 25.0 + - - +
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Residues in contact with ALA 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 4.0 5.6 - - - -
34J MET* 3.3 5.9 - - - +
35J TYR* 2.9 33.5 + - + +
37J TYR* 4.2 7.0 - - + -
93J CYS* 1.3 76.8 - - - +
95J SER* 1.3 61.8 + - - +
103J GLN* 3.7 29.4 - - + +
104J TYR 3.3 17.3 - - - +
105J PHE* 4.1 15.9 - - + -
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Residues in contact with SER 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ILE* 3.9 9.7 - - - +
27J GLN* 4.0 18.0 - - - +
29J LEU* 3.9 13.5 - - - +
31J HIS* 2.8 34.3 + - - -
33J ALA 3.2 13.7 - - - -
34J MET* 4.1 4.7 - - - -
35J TYR* 4.6 0.9 - - - -
94J ALA* 1.3 75.0 - - - +
96J SER* 1.3 58.8 + - - +
102J GLU 4.1 0.2 - - - +
103J GLN* 3.5 5.9 - - - -
104J TYR 3.0 30.5 + - - -
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Residues in contact with SER 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J HIS* 3.0 20.3 - - - +
33J ALA* 3.1 21.6 + - - +
35J TYR* 3.5 21.9 + - - -
95J SER* 1.3 72.6 - - - +
97J SER* 1.3 65.9 + - - +
98J ARG 3.2 19.9 + - - -
99J ALA* 4.1 0.2 - - - -
100J SER 4.6 0.3 + - - -
101J TYR* 3.7 13.1 + - - -
102J GLU 3.3 22.2 - - - -
103J GLN* 4.1 3.2 - - - +
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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