Contacts of the strand formed by residues 6 - 12 (chain A) in PDB entry 3EBV
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 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER 3.2 9.6 - - - +
3A LEU* 3.4 20.6 - - - +
4A LYS 3.9 0.4 - - - -
5A HIS* 1.3 73.2 - - - +
7A VAL* 1.3 65.9 + - - +
8A THR* 4.1 2.0 - - - +
31A ASP* 3.3 8.3 - - + +
32A ILE* 4.6 16.2 - - + -
266A ARG* 2.9 21.9 + - + +
267A GLY* 3.3 6.4 - - - -
268A ALA 3.1 23.6 + - - +
291A VAL* 3.6 2.3 - - - +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 1.3 77.5 - - - +
8A THR* 1.3 65.2 + - - +
29A ALA* 3.6 17.5 - - + +
30A TYR* 3.7 26.6 - - + -
31A ASP* 2.9 32.6 + - - -
32A ILE 3.2 5.8 + - - +
268A ALA 3.3 7.6 - - - +
283A TRP* 4.0 19.7 - - + -
284A SER* 5.7 1.1 - - - -
287A VAL* 4.8 2.2 - - + -
288A GLY* 3.9 22.2 - - - +
291A VAL* 3.9 26.7 - - + -
292A HIS* 4.2 3.4 - - - +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 5.2 1.9 - - - +
7A VAL* 1.3 76.0 - - - +
9A GLY* 1.3 67.6 + - - +
10A TYR* 4.7 4.0 - - + +
30A TYR* 3.9 2.2 - - - -
32A ILE* 3.2 42.1 - - + +
34A ALA* 4.5 12.6 - - + -
79A ILE* 5.5 1.6 - - + -
117A ASP* 6.5 0.2 - - - -
147A THR* 5.6 2.2 - - + +
175A VAL* 4.7 1.9 - - - +
177A ASN* 3.1 32.1 + - - +
268A ALA 2.9 7.9 + - - -
269A MSE 3.1 15.7 - - + -
270A THR 2.9 25.6 + - - -
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Residues in contact with GLY 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 1.3 75.5 - - - +
10A TYR* 1.3 65.9 + - - -
11A TRP 3.7 0.7 + - - -
30A TYR* 3.5 24.5 - - - -
32A ILE 2.9 9.1 + - - -
33A ILE* 3.4 7.6 - - - +
34A ALA 2.9 23.1 + - - -
270A THR 3.6 7.0 - - - -
273A THR* 3.9 7.1 - - - +
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Residues in contact with TYR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A THR* 4.7 3.5 - - + +
9A GLY* 1.3 73.0 - - - -
11A TRP* 1.3 58.9 + - - +
34A ALA* 3.3 25.1 - - + -
36A ALA* 4.2 8.5 - - + -
37A PHE* 4.5 0.4 - + - -
81A SER* 3.6 11.4 - - - -
117A ASP* 2.6 34.5 + - - -
119A ASP* 4.5 8.7 - - - -
149A ALA* 3.1 22.7 - - + +
177A ASN* 5.5 2.7 + - + +
181A TYR* 5.6 0.9 - - - -
269A MSE 3.7 34.0 - - + +
270A THR 3.1 21.8 + - - +
271A TRP* 3.3 42.2 - + + -
272A SER* 3.2 7.1 - - - -
273A THR* 2.8 30.5 + - - +
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Residues in contact with TRP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLY 3.7 1.6 + - - -
10A TYR* 1.3 71.1 - - - +
12A GLN* 1.3 68.3 + - - +
13A ASN* 3.9 16.8 - - + -
21A GLN* 2.9 37.6 + - + +
22A LYS 3.5 8.5 + - - -
23A ILE* 3.5 19.3 - - + -
26A VAL* 3.6 22.9 - - + -
33A ILE* 3.7 21.1 - - + -
34A ALA 2.8 10.5 + - - +
35A VAL* 3.9 18.8 - - + -
36A ALA* 2.9 26.0 + - - +
51A LEU* 3.9 13.9 - - + -
56A LEU* 3.8 22.4 - - + -
59A TYR* 3.7 15.9 - + - -
64A PHE* 3.8 18.6 - + - -
273A THR* 3.6 12.6 - - + +
274A ASN* 4.6 1.3 - - - +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TRP* 1.3 88.3 + - - +
13A ASN* 1.3 57.7 + - - +
14A PHE* 3.1 44.2 + - + +
15A ASN* 4.9 0.2 - - - +
16A ASN* 2.9 46.3 + - - +
18A ALA* 4.0 2.2 - - - +
21A GLN 5.1 0.2 - - - +
36A ALA* 3.9 4.7 - - - -
56A LEU* 4.0 7.3 - - - +
271A TRP* 4.2 6.9 - - + -
272A SER* 2.8 29.0 + - - +
274A ASN* 2.9 41.5 + - - +
275A TRP* 3.7 4.9 + - - -
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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