Contacts of the strand formed by residues 91 - 100 (chain B) in PDB entry 3K3K
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 THR 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASP* 6.3 0.9 - - - -
81B VAL 3.2 10.1 - - - -
82B ILE* 3.9 20.6 - - + -
83B VAL* 3.9 5.3 - - - +
89B ALA* 3.7 1.2 - - - +
90B ASN* 1.3 91.8 - - + +
92B SER* 1.3 63.1 + - - +
93B THR* 6.1 0.2 - - - -
113B GLY* 3.5 5.8 - - - -
114B GLU* 3.2 26.6 + - + +
115B HIS* 3.0 18.9 + - - -
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG 3.8 0.7 - - - +
80B ASP* 3.6 2.1 - - - -
81B VAL* 2.8 40.4 + - - +
91B THR* 1.3 78.2 - - - +
93B THR* 1.3 62.4 + - - +
94B GLU* 2.7 28.3 + - - -
110B ILE* 3.6 6.8 - - - +
112B GLY 3.6 6.3 - - - -
113B GLY* 4.1 0.7 - - - -
115B HIS* 3.3 18.7 - - - -
1001B A8S 3.6 17.0 - - - +
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Residues in contact with THR 93 (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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78B THR* 4.5 9.9 - - + +
79B ARG 3.4 6.1 - - - +
80B ASP* 3.2 24.5 + - - +
91B THR* 6.1 0.2 - - - -
92B SER* 1.3 72.4 - - - +
94B GLU* 1.3 59.1 + - - +
110B ILE* 3.5 4.3 - - - +
111B ILE* 2.7 50.7 + - + -
112B GLY* 2.9 26.7 + - - +
113B GLY* 4.3 2.8 + - - -
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Residues in contact with GLU 94 (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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52B PHE* 3.6 4.3 - - + -
59B LYS* 4.8 1.4 + - - -
78B THR* 3.1 7.8 - - - -
79B ARG* 2.8 77.8 + - + +
81B VAL* 3.7 16.1 - - - +
92B SER* 2.7 26.4 + - - +
93B THR* 1.3 79.0 - - - +
95B ARG* 1.3 62.0 + - - +
108B PHE* 3.8 29.4 - - + -
109B SER 3.3 4.7 - - - +
110B ILE* 4.0 10.7 - - + +
111B ILE* 4.4 2.2 - - - -
1001B A8S 4.3 11.1 + - - +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.9 2.9 - - - -
76B GLY* 3.9 20.4 - - - +
77B CYS 3.3 9.9 - - - +
78B THR* 4.1 9.0 - - + -
94B GLU* 1.3 74.7 - - - +
96B LEU* 1.3 72.4 + - - +
97B ASP* 2.8 28.3 + - - +
108B PHE* 3.2 2.8 - - - -
109B SER* 2.8 50.9 + - - +
111B ILE* 3.5 32.9 - - + +
121B LYS* 5.5 1.6 - - - +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 3.5 31.3 - - + -
73B MET* 3.7 23.8 - - + -
74B ARG 3.8 12.1 - - - +
75B VAL* 3.6 7.1 - - - +
76B GLY* 2.8 29.8 + - - +
77B CYS* 2.8 42.0 + - - +
95B ARG* 1.3 73.7 + - - +
97B ASP* 1.3 58.9 + - - +
98B ILE 3.5 26.2 - - - +
99B LEU* 4.4 11.2 - - + -
106B THR* 3.6 10.5 - - - +
107B GLY 3.5 11.2 - - - +
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Residues in contact with ASP 97 (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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75B VAL* 3.4 20.0 - - - +
95B ARG* 2.8 35.1 + - - +
96B LEU* 1.3 72.9 - - - +
98B ILE* 1.3 74.2 + - + +
107B GLY* 2.9 14.2 + - - +
108B PHE 3.1 18.2 + - - +
109B SER* 2.6 24.4 + - - -
121B LYS* 3.4 21.5 + - - +
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Residues in contact with ILE 98 (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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20B PHE* 5.2 8.5 - - + -
75B VAL* 3.9 4.7 - - - -
96B LEU* 3.5 5.1 - - - +
97B ASP* 1.3 92.3 - - + +
99B LEU* 1.3 66.2 + - - +
100B ASP* 4.4 7.4 - - + +
105B VAL* 3.8 29.4 - - + +
106B THR* 2.9 22.3 + - - -
107B GLY* 3.2 13.6 + - - +
121B LYS* 4.7 8.1 - - - +
123B VAL* 4.2 33.2 - - + -
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Residues in contact with LEU 99 (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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46B TRP* 4.0 22.0 - - + -
50B ARG* 3.9 33.0 - - + +
73B MET* 3.7 42.2 - - + +
74B ARG* 5.6 0.7 - - - -
75B VAL* 3.8 13.1 - - + +
96B LEU* 4.4 12.6 - - + -
98B ILE* 1.3 76.2 - - - +
100B ASP* 1.3 60.1 + - - +
101B ASP* 3.9 11.0 + - - +
105B VAL 3.6 1.6 - - - -
106B THR* 3.7 15.9 - - - +
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Residues in contact with ASP 100 (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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46B TRP* 3.6 2.5 - - - -
98B ILE* 4.6 6.7 - - + -
99B LEU* 1.3 75.9 - - - +
101B ASP* 1.3 57.4 + - - +
102B GLU* 3.0 24.6 + - - +
103B ARG* 3.1 34.4 + - - +
104B ARG* 2.8 26.3 + - - -
105B VAL* 2.9 28.9 + - + +
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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