Contacts of the strand formed by residues 92 - 99 (chain A) in PDB entry 1K4C
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 ALA 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.9 25.1 - - + -
39A GLN 3.4 22.2 - - - +
40A ARG* 3.8 7.2 - - - +
41A PRO* 4.7 4.9 - - - -
90A ASP 3.3 4.5 + - - +
91A SER* 1.3 77.5 - - - +
93A VAL* 1.3 66.6 + - - +
94A TYR* 3.5 9.6 - - + -
113A THR* 4.6 3.1 - - - -
114A VAL 2.9 30.0 + - - -
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Residues in contact with VAL 93 (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 VAL 3.8 1.0 - - - +
38A LYS* 3.6 2.6 - - - -
39A GLN* 2.9 40.4 + - + +
41A PRO* 5.7 1.1 - - + +
92A ALA* 1.3 76.4 - - - +
94A TYR* 1.3 61.8 + - - +
95A TYR* 3.7 35.6 + - + +
110A ALA 4.9 1.1 - - - +
111A GLY* 4.0 18.8 - - - -
112A THR 3.4 7.2 - - - +
113A THR* 3.8 21.8 - - + +
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Residues in contact with TYR 94 (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 GLN* 2.9 18.4 - - - +
20A LEU* 3.7 18.4 - - + -
36A TRP* 4.9 1.3 - - + -
37A VAL 3.4 1.8 - - - -
38A LYS* 3.7 28.5 + - + +
48A ILE* 3.5 33.0 - - + -
81A MET* 3.6 15.0 - - + -
83A LEU* 3.8 22.0 - - + +
90A ASP* 2.7 41.5 + - - +
92A ALA 3.5 20.4 - - - -
93A VAL* 1.3 72.9 - - - +
95A TYR* 1.3 61.4 + - - +
111A GLY* 4.3 0.2 - - - -
112A THR* 2.9 22.6 + - - +
114A VAL* 3.6 23.1 - - + -
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Residues in contact with TYR 95 (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 GLN* 3.6 3.4 - - - +
36A TRP* 3.2 9.8 - - - -
37A VAL* 2.8 41.4 + - + +
39A GLN* 3.5 26.4 + - + -
45A LEU* 4.6 6.3 - - + -
93A VAL* 3.7 22.5 - - + +
94A TYR* 1.3 73.5 - - - +
96A CYS* 1.3 61.8 + - - +
108A TRP* 3.7 31.0 - + + -
109A GLY 3.5 16.8 - - - -
110A ALA 3.5 19.2 + - - -
111A GLY* 3.6 9.9 - - - -
38B GLN* 3.2 23.5 + - - -
41B ASN 5.7 0.3 - - - -
42B GLY 3.3 9.2 + - - -
43B SER* 3.8 16.6 - - - -
44B PRO* 4.1 6.3 - - + -
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Residues in contact with CYS 96 (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 LEU* 3.9 12.6 - - - -
6A GLN* 3.2 32.1 - - - +
22A CYS* 2.7 45.3 - - + -
34A ILE* 4.6 2.2 - - + -
35A HIS 3.1 9.2 - - - +
36A TRP* 3.9 16.2 - - + -
95A TYR* 1.3 77.7 - - - +
97A ALA* 1.3 63.9 + - - +
108A TRP* 3.6 0.9 - - - -
109A GLY 2.9 24.1 + - - -
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Residues in contact with ALA 97 (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 LEU* 3.6 5.4 - - - -
34A ILE* 3.4 6.1 - - - +
35A HIS* 2.7 38.0 + - + +
37A VAL* 5.5 2.2 - - + -
96A CYS* 1.3 77.3 - - - +
98A ARG* 1.3 61.0 + - - +
105A PHE* 4.0 22.7 - - + -
107A VAL 3.3 14.4 - - - +
108A TRP* 4.0 24.2 - - + -
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Residues in contact with ARG 98 (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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3A GLN* 3.0 30.8 - - - +
4A LEU* 3.6 13.6 - - + +
24A ALA* 3.4 24.0 - - - +
25A SER 2.9 27.3 + - - +
26A GLY 4.7 1.2 - - - -
27A TYR 3.6 14.3 + - - -
28A THR* 4.0 9.7 - - - +
32A ASP* 4.6 7.4 + - + -
33A TRP 3.7 5.8 - - - +
34A ILE* 4.1 15.7 - - + +
97A ALA* 1.3 72.8 - - - +
99A GLU* 1.3 70.2 - - - +
100A ARG* 3.0 40.3 - - + +
105A PHE* 3.6 4.1 - - - -
106A ALA* 3.1 28.6 + - - +
107A VAL* 3.0 21.9 + - + -
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Residues in contact with GLU 99 (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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32A ASP* 3.5 2.6 - - - +
33A TRP* 2.9 37.4 + - - +
35A HIS* 2.8 26.8 + - + +
97A ALA 4.1 0.2 + - - -
98A ARG* 1.3 76.3 - - - +
100A ARG* 1.3 61.9 + - - +
101A GLY 3.0 11.7 + - - +
102A ASP 3.2 3.8 + - - -
103A GLY* 2.7 31.3 + - - +
104A TYR 3.4 24.2 - - - +
105A PHE* 4.3 4.0 - - + -
96B PHE* 3.9 7.6 - - + -
52C ARG* 2.7 44.7 + - - -
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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