Contacts of the strand formed by residues 5 - 13 (chain B) in PDB entry 4R7X
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 LYS 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLY* 1.3 76.1 - - - +
6B VAL* 1.3 66.5 + - - +
7B LYS* 5.2 2.2 - - - +
38B VAL* 3.6 1.9 - - - +
39B THR* 3.1 53.7 + - + +
42B ILE* 3.6 9.3 - - - +
144B ARG* 4.8 4.3 - - - +
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Residues in contact with VAL 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 1.3 77.3 - - - +
7B LYS* 1.3 64.8 + - - +
8B SER 3.7 25.1 - - - +
9B LEU* 4.8 5.6 - - + -
36B LEU* 3.7 14.6 - - + -
37B GLU 3.8 3.4 - - - +
38B VAL* 4.6 1.6 - - + +
42B ILE* 3.6 25.8 - - + -
142B LEU* 3.9 14.1 - - + -
144B ARG* 3.3 33.0 - - - +
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Residues in contact with LYS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 3.5 6.8 + - - +
6B VAL* 1.3 76.0 - - - +
8B SER* 1.3 59.2 + - - +
37B GLU* 2.9 50.4 + - + +
39B THR* 3.9 28.7 - - + -
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Residues in contact with SER 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 3.7 7.4 - - - +
7B LYS* 1.3 82.8 - - - +
9B LEU* 1.3 64.1 + - - +
10B THR* 3.6 21.3 + - - +
35B ASN 4.6 0.8 + - - -
36B LEU* 3.7 2.6 - - - -
37B GLU* 2.9 52.8 + - - +
109B ARG* 5.7 2.3 + - - -
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 5.1 8.0 + - - +
6B VAL* 4.8 4.9 - - + -
8B SER* 1.3 76.6 + - - +
10B THR* 1.3 65.5 + - - +
34B VAL* 4.2 19.3 - - + -
35B ASN 3.4 16.2 - - - +
36B LEU* 3.8 20.0 - - + -
47B LEU* 5.3 6.5 - - + -
140B ALA* 4.4 15.9 - - + +
141B GLU 5.8 0.2 - - - -
142B LEU* 4.5 20.0 - - + -
150B VAL* 4.5 21.5 - - + +
152B LEU* 3.2 41.3 - - + +
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 6.3 2.5 - - + -
8B SER* 3.6 17.5 + - - +
9B LEU* 1.3 80.2 - - - +
11B ILE* 1.3 71.5 + - - +
12B SER* 5.1 1.3 + - - -
34B VAL* 3.6 3.6 - - - +
35B ASN* 2.8 50.4 + - - +
109B ARG* 4.2 7.6 + - - -
152B LEU* 3.7 4.5 - - + -
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 5.1 2.5 - - - -
10B THR* 1.3 82.2 - - - +
12B SER* 1.3 60.8 + - - +
13B PHE* 4.1 12.1 - - + -
33B ARG 3.8 2.9 - - - -
34B VAL* 4.9 5.6 - - + -
114B PHE* 4.0 27.8 - - + -
138B VAL* 3.4 30.5 - - + +
139B LYS 4.4 0.4 - - - -
140B ALA* 3.9 22.2 - - + +
152B LEU* 3.5 31.2 - - + +
154B LYS* 2.6 51.9 + - + +
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 5.1 1.7 + - - -
11B ILE* 1.3 73.7 - - - +
13B PHE* 1.3 68.5 + - - +
14B ASP* 5.9 0.7 - - - -
32B GLY* 3.1 5.8 - - - -
33B ARG* 2.6 75.0 + - - +
35B ASN* 3.7 6.5 + - - -
109B ARG* 5.1 0.3 + - - -
114B PHE* 4.1 2.3 - - - -
154B LYS* 4.2 2.7 - - - +
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Residues in contact with PHE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.1 6.5 + - + -
12B SER* 1.3 79.9 - - - +
14B ASP* 1.3 64.0 + - - +
15B CYS* 3.4 15.4 + - - -
22B PRO* 3.7 26.0 - - + -
24B TYR* 4.0 10.3 - - - +
30B VAL* 4.2 13.0 - - + -
31B SER 3.8 6.3 - - - -
114B PHE* 4.0 22.0 - + - -
138B VAL* 4.1 15.9 - - + -
154B LYS* 3.8 46.9 - - + +
155B GLU 3.8 9.6 - - - -
156B PHE* 3.7 33.2 - + + -
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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