Contacts of the strand formed by residues 145 - 154 (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 ARG 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A HIS* 3.6 8.4 + - - -
56A CYS* 2.9 52.9 + - + +
57A ILE* 3.6 15.9 + - - +
59A ALA* 3.8 1.6 - - - +
60A GLY 2.9 31.0 + - - +
61A PRO* 4.5 0.6 - - - +
117A VAL* 3.8 14.4 - - + -
118A VAL 3.9 4.9 - - - -
119A HIS* 3.7 11.4 - - + -
143A GLY 4.7 0.7 - - - +
144A ALA* 1.3 74.3 - - - +
146A ALA* 1.3 62.1 + - - +
147A ALA 3.6 0.2 - - - -
160A SO4 2.5 44.4 + - - +
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Residues in contact with ALA 146 (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 GLY* 3.6 14.9 - - - -
11A GLU 4.2 3.6 + - - -
12A THR* 5.1 1.1 + - + +
13A VAL* 4.0 28.4 + - + +
37A LEU* 5.1 2.2 - - + -
56A CYS* 5.0 1.1 - - - -
118A VAL* 2.8 16.4 + - + +
119A HIS 4.3 2.9 - - - +
120A ALA* 4.3 20.0 - - + +
144A ALA* 3.5 2.2 + - - -
145A ARG* 1.3 74.5 - - - +
147A ALA* 1.3 63.4 + - - +
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Residues in contact with ALA 147 (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 LEU* 4.0 12.5 - - + +
9A ARG 3.3 16.2 - - - +
10A GLY* 4.2 0.2 - - - -
13A VAL* 3.5 32.3 - - + +
56A CYS* 3.5 6.3 - - - -
117A VAL* 3.4 6.8 - - - +
118A VAL* 3.0 32.5 + - + -
145A ARG 3.6 0.6 - - - -
146A ALA* 1.3 82.0 - - - +
148A CYS* 1.3 63.3 + - - +
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Residues in contact with CYS 148 (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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7A VAL 3.8 0.3 - - - +
8A LEU* 3.8 6.5 - - - -
9A ARG* 2.9 30.7 + - - +
52A SER* 5.2 9.2 - - - -
55A GLY 4.0 7.0 - - - -
56A CYS* 2.1 52.0 - - + -
59A ALA* 5.4 2.2 - - + -
115A SER* 5.0 5.4 - - - -
116A MET 3.1 12.3 - - - +
117A VAL* 3.9 13.7 - - + -
147A ALA* 1.3 74.4 - - - +
149A GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 149 (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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6A ALA* 4.0 5.7 - - - +
7A VAL 3.3 22.2 - - - -
8A LEU* 4.0 3.8 - - - +
50A GLY 5.6 0.2 - - - -
115A SER* 3.2 5.7 - - - -
116A MET* 2.9 32.6 + - - +
148A CYS* 1.3 76.8 - - - +
150A VAL* 1.3 65.2 + - - -
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Residues in contact with VAL 150 (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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5A VAL 3.3 8.3 - - - +
6A ALA* 3.4 8.1 - - - -
7A VAL 4.3 2.7 + - - +
50A GLY* 3.2 26.5 - - - +
52A SER* 5.0 9.4 - - - +
113A GLY* 3.9 16.8 - - - +
114A ARG 3.4 12.8 - - - +
115A SER* 4.4 0.4 - - - +
149A GLY* 1.3 72.1 - - - -
151A ILE* 1.3 70.4 + - - +
152A ALA* 3.2 13.9 + - + +
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Residues in contact with ILE 151 (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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4A ALA* 3.7 23.3 - - + -
5A VAL 3.8 5.6 - - - +
6A ALA* 4.3 4.0 - - + -
19A ILE* 4.2 15.5 - - + -
46A VAL* 4.0 10.3 - - + -
111A VAL* 3.5 46.2 - - + +
112A VAL* 3.8 9.2 - - + +
113A GLY* 2.8 29.6 + - - -
114A ARG 2.8 15.5 + - - +
115A SER 4.0 20.0 - - - +
116A MET* 4.0 23.3 - - + -
150A VAL* 1.3 71.5 - - - +
152A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 152 (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 ALA* 3.0 6.9 - - - -
5A VAL* 2.8 46.2 + - + +
112A VAL* 5.0 1.1 - - - -
150A VAL* 3.2 8.5 + - + +
151A ILE* 1.3 73.8 - - - +
153A LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 153 (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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2A ASN* 5.5 11.9 - - + +
3A ARG 3.9 16.4 - - - +
4A ALA* 4.5 1.6 - - - +
5A VAL* 5.3 0.5 - - - +
105A LEU* 6.2 1.1 - - + +
112A VAL* 4.4 31.0 - - + +
151A ILE 4.2 1.0 + - - -
152A ALA* 1.3 78.3 - - - +
154A ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 154 (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 ARG* 3.0 32.1 + - + +
4A ALA* 4.3 4.3 - - - -
5A VAL* 4.3 9.0 - - + -
18A TRP* 4.0 28.3 - - + -
153A LEU* 1.3 82.9 - - - +
155A ALA* 1.3 66.6 + - - +
156A PRO* 3.3 8.0 - - - +
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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