Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 1NPK
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 VAL 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ALA* 3.9 17.9 - - + -
15A VAL 3.4 12.3 - - - +
16A LYS* 4.3 0.7 - - - -
17A PRO* 3.7 27.4 - - + -
43A LYS 3.8 0.7 - - - +
44A GLN* 3.2 3.7 - - - +
45A LEU* 2.6 39.9 + - + +
47A PRO* 3.6 22.9 - - + -
72A ILE* 3.8 9.4 - - + +
76A PRO* 1.3 79.2 - - - +
78A VAL* 1.3 68.1 + - - +
79A ALA 3.8 1.2 + - - +
137A TRP* 3.9 25.8 - - + -
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Residues in contact with VAL 78 (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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13A LEU 3.9 0.3 - - - +
14A ALA* 3.2 2.3 - - - -
15A VAL* 2.8 49.1 + - + +
20A VAL* 4.0 3.9 - - + +
25A VAL* 4.0 36.8 - - + -
29A ILE* 4.8 0.2 - - + -
42A LEU* 3.7 28.5 - - + -
43A LYS 3.5 7.0 - - - +
44A GLN* 4.1 25.6 - - + +
77A VAL* 1.3 75.1 - - - +
79A ALA* 1.3 60.1 + - - +
80A MET* 4.0 9.0 + - - +
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Residues in contact with ALA 79 (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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12A PHE* 3.7 21.5 - - + -
13A LEU 3.5 5.6 - - - -
14A ALA* 4.2 2.2 - - - +
42A LEU* 3.4 2.8 - - - +
43A LYS* 2.9 32.9 + - + +
45A LEU* 3.9 12.3 - - + -
77A VAL 3.8 2.0 + - - -
78A VAL* 1.3 72.8 - - - +
80A MET* 1.3 63.5 + - - +
137A TRP* 3.9 22.9 - - + -
138A PHE* 3.5 12.6 - - + -
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Residues in contact with MET 80 (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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12A PHE* 3.5 8.7 - - - -
13A LEU* 2.7 68.1 + - + +
15A VAL* 3.6 29.4 - - + -
28A ILE* 3.7 20.9 - - + -
29A ILE* 3.7 28.9 - - + -
39A LEU* 3.9 6.3 - - + -
41A GLY 3.1 12.6 - - - +
42A LEU* 3.7 11.4 - - + -
78A VAL* 4.6 3.1 - - - -
79A ALA* 1.3 76.7 - - - +
81A VAL* 1.3 63.0 + - - +
82A PHE* 4.0 17.9 - - + -
121A ILE* 4.5 1.3 - - + -
138A PHE* 4.1 2.4 - - - -
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Residues in contact with VAL 81 (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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10A ARG* 3.9 11.4 - - + -
11A THR 3.3 11.0 - - - +
12A PHE* 4.2 2.5 - - + -
39A LEU* 3.8 4.7 - - - +
40A VAL* 2.9 49.6 + - + -
41A GLY 2.9 12.9 + - - +
80A MET* 1.3 79.3 - - - +
82A PHE* 1.3 64.0 + - - +
134A ILE* 3.6 36.3 - - + -
138A PHE* 3.6 27.4 - - + -
143A LEU* 3.9 10.1 - - + -
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Residues in contact with PHE 82 (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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10A ARG* 3.2 4.4 - - - +
11A THR* 2.9 37.8 + - + -
13A LEU* 3.9 17.9 - - + -
29A ILE* 4.2 17.9 - - + -
32A TYR* 3.4 36.1 - + + -
33A GLU* 4.4 4.5 - - + -
37A PHE* 3.6 24.5 - - + -
38A VAL 3.4 15.7 - - - -
39A LEU* 3.6 37.0 - - + -
80A MET* 4.0 22.2 - - + -
81A VAL* 1.3 78.2 - - - +
83A GLU* 1.3 59.5 + - - +
87A VAL* 3.8 18.8 - - + +
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Residues in contact with GLU 83 (chain A).
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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7A ASN 3.8 5.1 - - - +
8A LYS* 3.8 35.5 - - - +
9A GLU 3.2 11.7 - - - +
10A ARG* 2.8 40.8 + - + -
36A GLY 4.7 0.2 - - - +
37A PHE* 3.5 8.2 - - - -
38A VAL* 2.8 42.9 + - + +
40A VAL* 3.6 15.7 - - + +
82A PHE* 1.3 76.4 - - - +
84A GLY* 1.3 60.8 + - - +
87A VAL* 4.5 0.4 - - - -
145A THR 5.6 0.2 - - - +
147A VAL* 3.4 26.9 - - + +
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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