Contacts of the strand formed by residues 92 - 98 (chain N) in PDB entry 5VAI
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 92 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38N ARG* 3.9 11.4 - - - +
39N GLN 3.8 1.6 - - - +
40N ALA* 3.5 22.0 - - + -
41N PRO* 3.6 11.0 - - - -
90N ASP 3.3 4.2 + - - +
91N THR* 1.3 78.0 + - - +
93N VAL* 1.3 67.0 + - - +
94N TYR* 3.4 24.5 + - + -
123N GLN* 3.3 4.7 + - - +
124N VAL 2.9 31.2 + - - +
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Residues in contact with VAL 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 3.3 1.7 - - - -
39N GLN* 2.9 45.4 + - + +
40N ALA 5.2 0.4 - - - -
41N PRO* 5.2 9.4 - - + -
92N ALA* 1.3 75.8 - - - +
94N TYR* 1.3 59.5 + - - +
95N TYR* 3.3 41.6 + - + +
121N GLY 5.4 0.2 - - - -
122N THR 3.5 13.5 - - - +
123N GLN* 3.6 18.2 - - + +
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Residues in contact with TYR 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N GLU* 4.4 2.3 - - - +
20N LEU* 4.5 12.6 - - + -
36N TRP* 5.2 11.8 - - + -
37N VAL 4.0 3.8 - - - +
38N ARG* 3.3 32.8 + - + -
68N PHE* 5.2 6.0 - + - -
81N LEU* 4.7 13.0 - - + -
83N MET* 4.5 11.4 - - - -
90N ASP* 2.1 36.0 + - - +
91N THR* 4.3 0.2 - - - -
92N ALA* 3.4 27.3 + - + -
93N VAL* 1.3 72.3 - - - +
95N TYR* 1.3 65.1 + - - +
121N GLY* 3.4 0.9 - - - -
122N THR* 2.9 45.5 + - - +
124N VAL* 3.5 39.0 - - + +
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Residues in contact with TYR 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6N GLU* 4.3 2.7 - - - +
36N TRP* 3.7 7.4 - - - +
37N VAL* 2.8 40.6 + - + +
38N ARG 6.2 0.2 - - - -
39N GLN* 4.1 24.0 + - + -
45N LEU* 6.4 1.1 - - + -
93N VAL* 3.3 35.2 + - + +
94N TYR* 1.3 75.0 - - - +
96N CYS* 1.3 60.8 + - - +
97N ALA* 3.9 1.6 - - + +
118N ARG* 3.3 46.9 - - + +
119N GLY 5.1 0.9 - - - -
120N GLN 3.2 24.2 + - - -
121N GLY* 3.1 18.4 - - - -
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Residues in contact with CYS 96 (chain N).
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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4N LEU* 3.2 15.6 - - - +
6N GLU* 3.1 34.6 + - - +
22N CYS* 2.0 48.9 - - + -
34N MET* 5.2 0.7 - - - -
35N ASN 3.9 2.7 - - - -
36N TRP* 3.3 26.4 - - + -
79N LEU* 4.3 6.3 - - + -
95N TYR* 1.3 72.3 - - - +
97N ALA* 1.3 60.8 + - - +
118N ARG* 4.0 0.3 - - - -
119N GLY 3.8 8.7 + - - -
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Residues in contact with ALA 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU* 4.2 0.9 - - - -
34N MET* 3.7 6.2 - - - +
35N ASN* 2.6 49.1 + - - +
37N VAL* 5.1 7.0 - - + -
95N TYR* 3.9 3.2 + - + +
96N CYS* 1.3 75.0 - - - +
98N ARG* 1.3 61.3 + - - +
109N ASP* 4.6 5.6 - - + +
115N TYR* 3.9 16.4 - - + -
117N TYR 3.3 18.2 - - - +
118N ARG* 4.5 12.8 - - + +
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Residues in contact with ARG 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLU 2.8 25.7 + - - -
227B SER* 3.6 6.1 + - - -
4N LEU* 4.3 6.2 - - + +
27N PHE* 4.0 22.2 - - + +
32N TYR* 3.1 48.3 - - + -
33N LYS 3.7 4.9 - - - +
34N MET* 3.5 22.7 - - + -
35N ASN* 4.5 1.8 - - - -
97N ALA* 1.3 76.0 - - - +
99N CYS* 1.3 76.3 + - - +
100N PRO 3.2 11.5 + - - -
109N ASP* 5.4 0.4 - - - -
115N TYR* 2.6 30.0 + - - -
117N TYR* 3.1 56.4 + - + +
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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