Contacts of the strand formed by residues 150 - 156 (chain A) in PDB entry 1KR2
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A THR* 4.1 25.2 + - + +
8A GLU 2.9 10.5 + - - +
9A VAL* 3.3 7.0 - - + +
10A VAL* 2.8 23.1 + - - +
103A GLN* 3.6 7.6 - - - +
148A VAL 4.0 8.5 - - - +
149A PRO* 1.3 76.2 - - - +
151A VAL* 1.3 64.4 + - - +
152A LYS* 3.7 23.6 + - - +
180A ASN 6.0 2.2 - - - +
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Residues in contact with VAL 151 (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 VAL* 3.4 11.9 - - + +
12A LEU* 3.9 30.3 - - + -
99A LEU* 3.9 17.9 - - + +
102A HIS* 3.9 11.0 - - + -
103A GLN* 2.9 38.4 + - + +
106A LEU* 3.4 27.6 - - + -
150A LYS* 1.3 71.8 - - - +
152A LYS* 1.3 67.9 + - - +
181A TYR* 3.8 23.2 - - + +
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Residues in contact with LYS 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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7A THR* 6.0 1.1 - - - -
9A VAL* 3.6 35.7 - - + -
10A VAL 2.9 9.4 + - - +
11A LEU* 3.6 2.4 - - - +
12A LEU* 2.9 25.5 + - - +
35A MET* 5.0 1.3 - - + -
41A TYR* 5.0 9.3 + - - -
99A LEU* 4.5 3.4 - - - -
150A LYS* 4.2 20.7 - - + +
151A VAL* 1.3 77.7 - - - +
153A LEU* 1.3 62.0 + - - +
154A LEU 3.5 0.3 + - - -
181A TYR 2.6 31.7 + - - +
182A GLY* 4.0 9.9 - - - +
183A LEU 5.1 0.2 - - - +
184A ILE* 3.8 26.7 - - + -
209A ASN* 3.0 22.9 - - - +
211A HIS* 4.9 9.6 - - + +
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Residues in contact with LEU 153 (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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12A LEU* 3.4 16.2 - - + +
14A CYS* 4.1 22.7 - - + +
95A THR* 3.9 32.5 - - + -
99A LEU* 4.1 22.2 - - + +
152A LYS* 1.3 71.0 - - - +
154A LEU* 1.3 61.3 + - - +
155A CYS* 3.9 2.8 + - + -
159A LEU* 4.4 24.0 - - + -
163A PHE* 5.9 1.1 - - + -
169A TRP* 5.4 2.9 - - + -
177A ILE* 4.8 3.4 - - + -
182A GLY 3.1 16.8 + - - +
183A LEU* 3.3 22.4 - - + +
184A ILE* 2.7 32.7 + - - +
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Residues in contact with LEU 154 (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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11A LEU* 4.3 15.0 - - + -
12A LEU 2.7 21.8 + - - +
13A ALA* 3.7 16.0 - - + +
14A CYS 4.6 2.1 + - - +
27A LEU* 3.9 15.5 - - + +
28A PHE* 3.6 59.7 - - + +
31A ALA* 4.0 24.0 - - + -
152A LYS 3.5 1.2 + - - +
153A LEU* 1.3 74.5 - - - +
155A CYS* 1.3 80.0 + - - +
184A ILE* 3.4 13.9 - - + +
186A VAL* 4.1 8.5 - - + -
809A TAD 4.2 2.1 + - - +
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Residues in contact with CYS 155 (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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27A LEU* 5.1 3.8 - - - -
153A LEU* 4.5 7.2 - - + -
154A LEU* 1.3 81.5 - - - +
156A GLY* 1.3 70.2 + - - +
159A LEU* 3.9 28.5 - - + -
160A LEU 4.8 1.3 - - - -
183A LEU* 4.3 21.5 - - - -
184A ILE 2.8 16.5 + - - +
185A CYS* 3.3 10.2 - - - -
186A VAL* 2.9 26.5 + - - +
809A TAD 3.0 23.3 - - - +
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Residues in contact with GLY 156 (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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155A CYS* 1.3 81.2 - - - +
157A ALA* 1.3 66.4 + - - -
158A ASP 3.4 2.5 - - - -
159A LEU 3.3 9.0 + - - -
160A LEU 3.4 8.1 + - - -
185A CYS* 3.6 10.3 - - - -
186A VAL 3.3 11.9 - - - -
809A TAD 3.1 34.8 + - - -
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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