Contacts of the helix formed by residues 200 - 211 (chain Y) in PDB entry 1KKC
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 ASN 200 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93Y LYS 3.0 17.5 + - - +
94Y ASN* 2.8 30.3 + - - +
95Y LEU 3.5 14.4 + - - +
96Y ALA* 3.8 16.3 - - + +
100Y SER 5.1 3.3 - - - +
101Y GLY* 4.7 4.7 - - - +
198Y VAL 3.4 1.2 + - - -
199Y ILE* 1.3 70.2 - - - +
201Y TRP* 1.3 60.8 + - - +
202Y ALA* 3.3 21.2 + - - +
203Y GLU* 3.2 21.8 + - - +
204Y ALA* 3.2 11.1 + - - +
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Residues in contact with TRP 201 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Y GLY 4.5 3.2 + - - -
103Y GLY* 3.8 6.8 + - - -
104Y LYS 3.6 23.1 - - - +
105Y ILE* 3.4 40.8 - - + +
107Y GLN 4.5 0.4 - - - -
108Y ALA* 3.4 21.0 - - + +
111Y LEU* 3.8 29.8 - - + -
115Y ILE* 4.1 5.8 - - + -
122Y PHE* 3.5 35.5 - + - -
125Y PHE* 4.1 4.7 - + - -
171Y PHE* 3.6 31.9 - + - -
196Y TRP* 3.6 22.7 + + - -
199Y ILE* 3.1 39.6 + - + +
200Y ASN* 1.3 69.6 + - - +
202Y ALA* 1.3 60.3 + - - +
204Y ALA* 3.6 5.5 - - + +
205Y GLU* 2.8 24.8 + - - +
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Residues in contact with ALA 202 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y SER 6.1 0.2 - - - +
101Y GLY 5.4 0.4 + - - -
107Y GLN* 4.0 35.0 + - + +
200Y ASN* 3.2 12.2 - - - +
201Y TRP* 1.3 77.6 - - - +
203Y GLU* 1.3 62.2 + - - +
205Y GLU* 3.4 15.3 - - - +
206Y ASN* 3.4 16.0 + - - +
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Residues in contact with GLU 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Y LYS* 3.5 30.3 + - - +
94Y ASN* 4.3 1.8 - - - -
200Y ASN* 3.2 28.9 + - - +
202Y ALA* 1.3 77.1 - - - +
204Y ALA* 1.3 66.0 + - - +
206Y ASN* 3.2 14.0 + - - +
207Y ARG* 2.7 65.2 + - - +
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Residues in contact with ALA 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Y ASN* 5.4 0.2 - - - +
111Y LEU* 3.5 21.5 - - + -
170Y VAL* 3.5 31.0 - - + +
171Y PHE* 4.4 10.1 - - + -
199Y ILE* 5.6 0.4 - - + -
200Y ASN 3.2 10.0 + - - +
201Y TRP* 3.3 17.5 + - + +
203Y GLU* 1.3 78.5 - - - +
205Y GLU* 1.3 56.4 + - - +
207Y ARG* 3.4 0.8 + - - -
208Y TYR* 2.9 31.5 + - - +
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Residues in contact with GLU 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107Y GLN 4.1 5.4 - - - +
108Y ALA* 3.4 16.3 - - + -
109Y PRO* 3.0 14.3 - - + +
110Y VAL* 2.9 36.5 + - - +
111Y LEU* 2.8 33.0 + - - +
201Y TRP 2.8 13.9 + - - +
202Y ALA 3.4 11.7 - - - +
204Y ALA* 1.3 76.7 - - - +
206Y ASN* 1.3 62.9 + - - +
208Y TYR* 3.2 2.9 + - - +
209Y ILE* 2.9 47.6 + - + +
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Residues in contact with ASN 206 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202Y ALA 3.4 13.7 + - - +
203Y GLU* 3.2 18.5 + - - +
205Y GLU* 1.3 86.7 - - - +
207Y ARG* 1.3 58.4 + - + +
209Y ILE* 3.8 9.4 - - - +
210Y ALA* 2.9 32.3 + - - +
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Residues in contact with ARG 207 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Y LEU* 2.8 51.4 + - - +
93Y LYS* 3.4 23.4 - - - +
94Y ASN* 3.1 24.0 - - - +
143Y TRP* 5.9 0.6 - - - -
146Y THR* 4.7 1.7 - - - +
168Y ALA* 5.1 1.6 - - - +
169Y PRO* 3.4 25.4 + - - +
170Y VAL* 3.1 30.0 + - - +
171Y PHE* 3.9 0.8 - - - +
203Y GLU* 2.7 42.9 + - - +
204Y ALA 3.7 6.3 - - - +
206Y ASN* 1.3 76.6 - - + +
208Y TYR* 1.3 53.5 - - - +
210Y ALA* 3.8 3.7 - - - +
211Y GLY* 2.7 33.1 + - - -
212Y ASP 4.4 1.2 + - - -
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Residues in contact with TYR 208 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y VAL* 3.9 20.6 - - + -
111Y LEU* 3.7 29.8 - - + -
114Y ALA* 3.3 33.9 - - + +
146Y THR* 3.3 21.3 - - - -
148Y GLY 3.9 0.2 - - - +
149Y PRO* 3.7 0.3 - - - +
150Y LYS* 2.9 42.0 + - - +
151Y GLY 2.6 33.8 + - - -
153Y LEU* 3.4 20.9 - - + -
170Y VAL* 4.3 10.0 - - + +
204Y ALA 2.9 17.3 + - - +
205Y GLU* 3.6 3.8 - - - +
207Y ARG* 1.3 77.6 - - - +
209Y ILE* 1.3 61.8 + - - +
211Y GLY* 3.3 9.2 + - - -
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Residues in contact with ILE 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Y VAL* 4.1 31.0 - - + -
149Y PRO* 3.1 19.9 - - - +
150Y LYS* 3.8 22.3 + - + +
205Y GLU* 2.9 42.2 + - + +
206Y ASN* 3.9 10.1 - - - +
208Y TYR* 1.3 74.8 - - + +
210Y ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149Y PRO* 3.3 14.3 - - - +
206Y ASN 2.9 20.0 + - - +
207Y ARG* 3.8 4.7 - - - +
209Y ILE* 1.3 79.3 - - - +
211Y GLY* 1.3 67.2 + - - +
212Y ASP* 3.4 12.3 - - + +
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Residues in contact with GLY 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146Y THR* 4.0 1.1 - - - -
148Y GLY* 3.6 12.4 - - - -
149Y PRO* 3.5 29.6 - - - +
168Y ALA* 3.7 13.2 - - - +
207Y ARG 2.7 21.0 + - - -
208Y TYR 3.3 4.3 + - - -
210Y ALA* 1.3 75.7 - - - +
212Y ASP* 1.3 59.5 + - - +
213Y LYS* 3.7 4.5 + - - +
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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