Contacts of the strand formed by residues 150 - 156 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C THR* 4.0 27.0 + - + +
8C GLU 2.9 11.5 + - - +
9C VAL* 3.3 8.1 - - + +
10C VAL* 2.9 22.9 + - - +
103C GLN* 3.5 8.7 - - - +
148C VAL 4.3 6.5 - - - +
149C PRO* 1.3 76.5 - - - +
151C VAL* 1.3 63.5 + - - +
152C LYS* 3.7 26.0 + - + +
180C ASN 6.1 0.9 - - - +
181C TYR* 5.6 1.1 - - - +
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.2 15.5 - - + +
12C LEU* 3.7 37.5 - - + -
99C LEU* 3.8 15.5 - - + +
102C HIS* 4.3 8.3 - - + -
103C GLN* 2.9 43.8 + - + +
106C LEU* 4.3 13.4 - - + +
149C PRO 4.0 0.2 + - - -
150C LYS* 1.3 74.6 - - - +
152C LYS* 1.3 68.4 + - - +
181C TYR* 3.7 24.5 - - + +
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Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C THR* 6.1 0.2 - - - -
9C VAL* 3.8 34.1 - - + -
10C VAL 2.8 8.2 + - - +
11C LEU* 3.6 2.3 - - - -
12C LEU* 2.9 25.6 + - - -
35C MET* 5.0 4.7 - - - -
41C TYR* 5.0 11.8 + - - -
99C LEU* 4.4 4.9 - - - -
150C LYS* 4.1 23.2 - - + +
151C VAL* 1.3 79.9 - - - +
153C LEU* 1.3 61.9 + - - +
154C LEU 3.5 0.2 + - - -
181C TYR 2.5 30.5 + - - +
182C GLY* 3.9 10.1 - - - +
184C ILE* 3.8 26.7 - - + -
209C ASN* 3.1 22.6 - - - +
211C HIS* 5.1 6.9 + - - -
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU 3.4 15.5 - - - +
14C CYS* 4.1 21.3 - - + +
95C THR* 3.7 32.3 - - + -
99C LEU* 4.1 18.8 - - + +
152C LYS* 1.3 71.8 - - - +
154C LEU* 1.3 62.5 + - - +
155C CYS* 3.9 2.6 + - + -
159C LEU* 4.3 21.8 - - + -
169C TRP* 5.1 3.4 - - + -
177C ILE* 4.6 6.7 - - + -
182C GLY 3.1 15.7 + - - +
183C LEU* 3.3 28.2 - - + +
184C ILE* 2.8 32.2 + - - +
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Residues in contact with LEU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.4 12.1 - - + -
12C LEU 2.8 20.6 + - - +
13C ALA* 3.5 21.6 - - + +
14C CYS 4.4 1.9 + - - -
27C LEU* 3.9 26.9 - - + +
28C PHE* 3.7 46.9 - - + -
31C ALA* 3.9 24.0 - - + -
152C LYS 3.5 1.2 + - - -
153C LEU* 1.3 73.1 - - - +
155C CYS* 1.3 70.3 + - - +
184C ILE* 3.4 17.9 - - + +
186C VAL* 4.0 13.7 - - + -
811C TAD 4.2 2.3 + - - +
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Residues in contact with CYS 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 4.7 4.9 - - - +
153C LEU* 4.6 4.5 - - + -
154C LEU* 1.3 79.0 - - - +
156C GLY* 1.3 70.2 + - - +
159C LEU* 3.9 28.5 - - + -
160C LEU 4.6 3.6 - - - -
183C LEU* 4.3 23.1 - - - -
184C ILE 3.0 15.6 + - - +
185C CYS* 3.4 14.3 - - - -
186C VAL* 2.9 24.9 + - - +
811C TAD 3.1 21.1 - - - +
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Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C CYS* 1.3 78.1 - - - +
157C ALA* 1.3 66.4 + - - -
158C ASP 3.2 3.4 - - - -
159C LEU* 3.1 11.4 + - - +
160C LEU 3.3 8.1 + - - -
185C CYS* 3.6 7.0 - - - -
186C VAL 3.2 12.3 - - - -
811C TAD 3.1 34.7 + - - -
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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