Contacts of the strand formed by residues 76 - 84 (chain A) in PDB entry 3KNB
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 GLY 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS* 4.3 2.9 - - - -
74A ASP 3.6 1.2 + - - -
75A GLY* 1.3 74.4 - - - -
77A LEU* 1.3 59.8 + - - -
78A TYR* 3.3 12.8 - - - -
94A ASN* 3.6 10.1 + - - -
95A ILE 2.9 32.2 + - - -
101A SO4 3.7 18.2 - - - -
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Residues in contact with LEU 77 (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 SER 5.3 0.7 - - - +
41A CYS* 3.9 15.3 - - - -
42A GLY 4.4 2.9 + - - -
76A GLY* 1.3 70.3 - - - -
78A TYR* 1.3 59.5 + - - +
79A THR* 3.9 4.2 + - - +
92A THR* 2.9 36.7 - - + +
93A VAL 3.8 0.7 - - - -
94A ASN* 3.7 32.5 + - + +
101A SO4 3.1 18.8 + - - +
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Residues in contact with TYR 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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39A TRP* 4.4 7.9 - + + -
40A SER 3.3 4.3 - - - -
41A CYS* 3.6 20.6 - - + +
46A ILE* 3.3 34.5 - - + -
54A PHE* 3.5 26.4 - + - -
65A LEU* 3.9 18.4 - - + -
67A ILE* 4.0 4.0 - - + +
74A ASP* 2.6 33.1 + - - -
76A GLY 3.3 14.4 - - - -
77A LEU* 1.3 73.9 - - - +
79A THR* 1.3 57.4 + - - +
80A LEU 4.2 0.2 + - - -
92A THR* 2.7 25.0 - - - +
93A VAL* 2.8 37.9 + - + +
95A ILE* 3.5 25.8 - - + -
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Residues in contact with THR 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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38A THR 3.6 1.7 - - - +
39A TRP* 3.3 8.9 - - - -
40A SER* 2.9 45.5 + - - +
77A LEU* 3.9 4.1 + - - +
78A TYR* 1.3 74.4 - - - +
80A LEU* 1.3 65.3 + - - +
81A SER* 3.5 21.8 - - - +
90A SER* 4.2 10.8 - - - -
91A ALA 3.4 10.5 - - - +
92A THR* 2.9 20.0 + - - +
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Residues in contact with LEU 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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8A ILE* 3.4 23.3 - - + +
11A LEU* 4.6 4.0 - - + -
27A CYS* 3.8 27.6 - - + -
29A PHE* 5.6 2.0 - - + -
37A VAL* 3.6 31.2 - - + -
38A THR 3.5 3.8 - - - +
39A TRP* 3.8 32.6 - - + +
63A THR* 3.8 19.5 - - + -
78A TYR 4.2 0.4 + - - -
79A THR* 1.3 72.9 - - - +
81A SER* 1.3 67.3 + - - +
82A LEU* 4.2 6.5 - - + -
90A SER* 3.1 5.7 - - - -
91A ALA 2.9 32.7 + - - +
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Residues in contact with SER 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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36A GLU 3.7 0.3 - - - +
37A VAL* 3.6 0.2 - - - -
38A THR* 2.8 45.7 + - - -
40A SER* 5.3 1.9 + - - -
79A THR* 3.5 19.4 - - - +
80A LEU* 1.3 73.7 - - - +
82A LEU* 1.3 70.9 + - - +
89A ASP 3.4 7.6 - - - -
90A SER* 4.0 6.3 - - - -
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Residues in contact with LEU 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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6A PRO* 3.5 27.4 - - + -
7A LYS 4.0 4.7 - - - -
8A ILE* 3.5 26.5 - - + -
29A PHE* 3.4 39.0 - - + -
35A PRO* 3.8 6.5 - - + -
36A GLU 3.2 4.5 - - - +
37A VAL* 3.7 27.1 - - + -
80A LEU* 4.2 11.7 - - + -
81A SER* 1.3 86.9 - - - +
83A GLY* 1.3 59.3 + - - +
88A SER* 3.1 7.8 - - - -
89A ASP 2.9 32.2 + - - +
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Residues in contact with GLY 83 (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 PRO* 3.8 4.0 - - - -
35A PRO* 3.3 1.8 - - - +
36A GLU* 2.9 40.0 + - - +
82A LEU* 1.3 76.0 - - - +
84A ASN* 1.3 60.0 + - - -
87A GLY 3.5 8.3 - - - -
88A SER* 4.3 3.8 - - - -
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Residues in contact with ASN 84 (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 ILE 3.0 24.6 + - - -
6A PRO* 3.3 15.7 - - - +
31A GLY* 4.1 1.0 - - - -
32A GLU 3.5 9.5 + - - +
33A PRO* 2.9 35.5 + - + +
34A THR 4.6 1.8 - - - +
35A PRO* 4.2 4.5 - - + -
36A GLU* 5.9 1.3 - - - -
83A GLY* 1.3 74.8 - - - +
85A GLU* 1.3 61.6 + - - +
86A PHE* 2.8 21.9 + - - +
87A GLY* 3.0 24.7 + - - +
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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