Contacts of the strand formed by residues 82 - 88 (chain A) in PDB entry 3KBF
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 ASP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A HIS* 4.4 4.0 - - - -
62A HIS* 3.2 4.9 + - - -
70A HIS* 3.1 9.1 + - + -
71A GLY 2.9 33.1 + - - +
72A GLY 4.7 0.4 - - - -
73A PRO* 3.6 12.5 - - - +
78A ARG* 3.5 22.9 + - + +
79A HIS* 2.8 37.9 + - - +
80A VAL 3.2 2.0 + - - -
81A GLY* 1.3 75.5 - - - +
83A LEU* 1.3 59.7 + - - +
84A GLY 3.4 2.0 - - - +
159A ZN 2.0 36.4 - - - -
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Residues in contact with LEU 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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30A ILE* 4.0 20.4 - - + -
44A PHE* 3.3 45.2 + - + +
46A VAL* 4.3 9.2 - - + +
73A PRO* 3.6 15.7 - - + +
78A ARG* 4.5 0.9 - - - +
81A GLY 3.1 12.4 + - - +
82A ASP* 1.3 76.1 - - - +
84A GLY* 1.3 62.5 + - - +
85A ASN 3.8 4.7 + - - +
86A VAL* 5.8 0.2 - - - +
98A LEU* 4.2 22.9 - - + +
100A ASP* 3.8 31.0 - - + +
103A VAL* 4.2 8.5 - - + -
116A MET* 4.0 24.9 - - + -
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Residues in contact with GLY 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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43A GLY* 3.6 3.5 - - - -
44A PHE* 2.9 28.1 + - - +
72A GLY* 5.0 0.2 - - - -
73A PRO* 3.5 20.7 - - - +
82A ASP* 3.4 4.9 - - - +
83A LEU* 1.3 78.1 - - - +
85A ASN* 1.3 64.4 + - - -
123A ASP* 4.1 10.0 + - - +
125A LEU* 4.0 13.2 - - - -
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Residues in contact with ASN 85 (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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41A LEU* 4.1 23.0 - - + +
42A HIS 3.2 4.1 - - - +
43A GLY 3.3 13.5 + - - -
83A LEU 3.8 3.7 + - - +
84A GLY* 1.3 76.4 - - - -
86A VAL* 1.3 66.4 + - - +
98A LEU* 5.6 5.5 - - - +
122A GLN* 3.6 17.8 - - - +
123A ASP* 2.8 49.3 + - - +
125A LEU* 4.0 11.1 - - - +
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Residues in contact with VAL 86 (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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34A ILE* 4.7 0.9 - - + -
37A LEU* 4.6 3.1 - - + -
40A GLY 3.7 0.9 - - - +
41A LEU* 3.4 5.2 - - - -
42A HIS* 2.8 50.9 + - + +
44A PHE* 3.7 24.9 - - + -
85A ASN* 1.3 77.7 - - - +
87A GLU* 1.3 60.0 + - - +
88A ALA 4.0 0.2 + - - -
94A ALA* 4.0 16.6 - - + -
95A LYS 5.6 0.7 - - - +
96A ILE* 3.6 40.2 - - + -
98A LEU* 5.2 4.5 - - + -
118A VAL* 4.4 14.1 - - + -
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Residues in contact with GLU 87 (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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40A GLY* 3.5 10.1 - - - +
41A LEU* 3.7 24.0 - - + +
86A VAL* 1.3 75.6 - - - +
88A ALA* 1.3 70.7 + - - +
89A GLY* 3.9 1.4 + - - -
93A VAL 4.0 0.5 - - - +
94A ALA* 3.4 17.5 - - - +
95A LYS 4.2 6.5 + - - +
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Residues in contact with ALA 88 (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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37A LEU* 3.7 28.9 - - + -
38A THR 3.5 22.9 - - - +
39A PRO* 3.5 2.3 - - + +
40A GLY 2.9 28.5 + - - +
42A HIS* 4.4 0.8 - - + -
86A VAL 4.0 0.6 + - - -
87A GLU* 1.3 78.5 - - - +
89A GLY* 1.3 61.5 + - - +
92A GLY 4.0 12.8 - - - -
93A VAL 3.4 7.2 - - - +
94A ALA* 3.9 1.7 - - - +
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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