Contacts of the strand formed by residues 4 - 11 (chain A) in PDB entry 3QEV
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 PHE 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.8 15.0 - - + -
2A LYS 3.9 5.6 - - - -
3A GLU* 1.3 79.2 - - - +
5A TYR* 1.3 74.8 + - - +
6A LEU* 4.1 1.8 - - + -
19A TYR* 3.4 1.0 - - - +
20A ILE* 2.9 61.9 + - + -
97A TYR* 3.5 11.4 - - - -
101A ILE* 3.8 23.8 - - + -
102A LYS 3.8 13.9 - - - +
103A TYR* 3.7 15.9 - - + -
104A ASP* 3.4 36.6 - - + -
107A LYS* 4.3 2.0 - - + -
108A ILE* 3.9 20.6 - - + -
349A TYR* 3.7 7.6 - + + -
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Residues in contact with TYR 5 (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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4A PHE* 1.3 80.1 - - - +
6A LEU* 1.3 68.3 + - - +
7A THR* 4.3 7.4 - - - +
8A VAL* 5.2 0.9 - - + -
17A GLU* 3.2 23.1 - - + +
18A ARG 3.8 3.4 - - - +
19A TYR* 3.8 0.4 - - - -
93A LEU* 3.7 35.4 - - + -
97A TYR* 3.4 16.0 + + + -
101A ILE* 3.4 29.8 - - + -
348A GLY 3.2 11.6 + - - -
349A TYR* 2.7 53.9 + + - -
352A LYS* 3.4 5.7 - - + -
353A ILE 2.7 39.9 + - - -
354A GLN* 4.9 3.8 - - - -
355A ILE* 4.6 4.9 - - + -
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Residues in contact with LEU 6 (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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4A PHE* 4.1 1.6 - - + -
5A TYR* 1.3 89.5 - - - +
7A THR* 1.3 66.4 + - + +
18A ARG* 2.7 18.8 + - + +
19A TYR* 3.8 23.6 - - - +
20A ILE* 3.8 20.6 - - + -
26A GLU* 3.8 35.9 - - + +
107A LYS 5.2 0.4 - - - +
108A ILE* 3.8 31.2 - - + -
211A VAL* 3.8 35.5 - - + +
269A SER* 4.6 2.6 + - - -
349A TYR* 3.9 6.3 + - - +
354A GLN* 6.2 0.2 - - - -
355A ILE* 4.5 10.9 + - - +
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Residues in contact with THR 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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5A TYR* 4.7 4.9 - - - +
6A LEU* 1.3 85.8 + - + +
8A VAL* 1.3 62.8 + - - +
9A GLU* 5.4 1.1 - - - -
17A GLU* 3.4 7.4 - - - +
18A ARG* 3.0 54.5 + - - +
211A VAL* 4.1 19.1 - - + +
245A HIS* 4.6 1.6 + - - -
267A GLY* 3.3 33.8 + - - +
268A ILE 4.4 0.7 - - - -
269A SER* 4.0 18.8 - - - +
354A GLN* 6.3 2.2 - - - +
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Residues in contact with VAL 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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5A TYR* 5.3 1.6 - - + -
7A THR* 1.3 77.9 - - - +
9A GLU* 1.3 68.4 + - - +
15A ILE* 3.5 27.4 - - + -
16A PHE 3.4 5.6 - - - +
17A GLU* 4.6 2.0 - - + -
89A LYS* 4.0 22.3 - - + +
92A TYR* 3.9 19.5 - - + -
93A LEU* 3.9 33.7 - - + -
354A GLN* 2.8 46.5 - - + +
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Residues in contact with GLU 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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7A THR* 5.4 1.2 - - - -
8A VAL* 1.3 83.9 + - - +
10A GLN* 1.3 59.9 + - - +
11A ILE* 4.0 8.3 - - + -
15A ILE* 3.3 12.4 - - - +
16A PHE* 2.8 37.4 + - + +
89A LYS* 4.2 7.7 - - - -
245A HIS* 4.3 3.4 - - + +
264A THR* 5.7 2.4 - - - +
265A LEU 4.3 0.5 - - - +
266A PHE* 3.5 36.4 - - + -
267A GLY* 2.8 39.7 + - - +
268A ILE 4.3 8.8 - - - +
354A GLN* 3.3 14.4 - - - +
356A GLN* 4.6 4.9 + - - -
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Residues in contact with GLN 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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9A GLU* 1.3 73.5 + - - +
11A ILE* 1.3 68.6 + - - +
12A GLY* 3.2 25.0 + - - +
14A SER 3.5 3.4 - - - -
15A ILE* 4.2 9.4 - - + -
65A MET* 3.7 36.1 - - + +
66A ARG* 5.2 2.8 - - - +
69A SER* 5.4 2.0 + - - -
87A ASP* 5.6 0.5 - - - +
88A PHE* 3.6 24.7 + - - +
89A LYS* 4.0 19.6 + - + +
247A LYS* 4.9 0.9 - - - -
266A PHE* 3.8 14.6 - - - -
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Residues in contact with ILE 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 GLU* 4.0 3.1 + - + -
10A GLN* 1.3 77.4 - - - +
12A GLY* 1.3 65.7 + - - +
13A ASP 3.3 0.7 + - - -
14A SER* 2.9 26.2 + - - +
16A PHE* 3.5 35.3 - - + -
245A HIS* 3.8 29.4 - - + +
247A LYS* 3.6 42.8 - - + +
266A PHE* 4.0 12.6 - - + -
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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