Contacts of the helix formed by residues 200 - 211 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS 3.1 15.9 + - - +
94A ASN* 2.8 30.0 + - - +
95A LEU 3.5 15.4 + - - +
96A ALA* 3.8 15.5 - - + +
100A SER 5.0 4.7 - - - +
101A GLY* 4.7 4.6 - - - +
198A VAL 3.3 2.4 + - - -
199A ILE* 1.3 69.6 - - - +
201A TRP* 1.3 61.1 + - - +
202A ALA* 3.3 12.1 + - - +
203A GLU* 3.1 30.8 + - - +
204A ALA* 3.2 9.7 + - - +
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Residues in contact with TRP 201 (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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101A GLY 4.4 3.6 + - - +
103A GLY* 3.7 10.8 + - - -
104A LYS 3.5 19.3 - - - +
105A ILE* 3.4 45.6 - - + +
107A GLN 4.7 0.2 - - - -
108A ALA* 3.4 14.6 - - + +
111A LEU* 3.9 20.6 - - + -
115A ILE* 4.3 4.7 - - + -
122A PHE* 3.5 32.8 - + - -
125A PHE* 4.1 4.9 - + - -
171A PHE* 3.6 33.2 - + - -
196A TRP* 3.7 21.4 + + - -
199A ILE* 2.9 42.1 + - + +
200A ASN* 1.3 68.1 - - - +
202A ALA* 1.3 60.8 + - - +
204A ALA* 3.0 14.6 + - + +
205A GLU 2.8 26.5 + - - -
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Residues in contact with ALA 202 (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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101A GLY* 5.3 1.1 + - - +
107A GLN* 4.0 37.5 + - + +
200A ASN* 3.2 10.1 + - - +
201A TRP* 1.3 77.8 - - - +
203A GLU* 1.3 62.3 + - - +
205A GLU* 3.4 3.9 + - - +
206A ASN* 3.3 27.4 + - - +
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Residues in contact with GLU 203 (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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93A LYS* 3.4 30.4 - - - +
94A ASN* 4.4 1.6 - - - -
200A ASN* 3.1 33.0 + - - +
202A ALA* 1.3 74.4 - - - +
204A ALA* 1.3 65.2 + - - +
206A ASN* 3.3 13.7 + - - +
207A ARG* 3.0 62.7 + - - +
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Residues in contact with ALA 204 (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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94A ASN* 5.5 0.6 - - + +
111A LEU* 3.5 21.3 - - + -
170A VAL* 3.6 27.1 - - + +
171A PHE* 4.5 7.9 - - + -
199A ILE* 5.5 0.4 - - + -
200A ASN 3.2 6.4 + - - +
201A TRP* 3.0 25.3 + - + +
203A GLU* 1.3 79.5 - - - +
205A GLU* 1.3 63.0 + - - +
207A ARG* 3.2 0.9 + - - +
208A TYR* 3.0 25.3 + - - +
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Residues in contact with GLU 205 (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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107A GLN 4.1 6.5 - - - +
108A ALA* 3.4 20.4 - - + -
109A PRO* 3.2 10.7 - - + +
110A VAL* 2.7 37.6 + - - +
111A LEU* 2.8 32.4 + - - +
201A TRP 2.8 12.9 + - - +
202A ALA 3.5 9.9 - - - +
203A GLU 3.2 0.2 - - - -
204A ALA* 1.3 77.1 - - - +
206A ASN* 1.3 67.0 + - - +
208A TYR* 3.4 1.7 + - - +
209A ILE* 3.0 41.3 + - + +
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Residues in contact with ASN 206 (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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202A ALA 3.3 15.0 + - - +
203A GLU* 3.3 18.5 + - - +
204A ALA 3.3 0.6 - - - -
205A GLU* 1.3 85.1 - - - +
207A ARG* 1.3 57.3 + - + +
209A ILE* 3.5 8.5 + - - +
210A ALA* 3.0 30.1 + - - +
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Residues in contact with ARG 207 (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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90A LEU* 2.8 50.8 + - - +
93A LYS* 3.5 22.6 - - - +
94A ASN* 3.1 26.0 - - - +
143A TRP* 5.9 0.2 - - - -
146A THR* 4.8 1.6 - - - +
168A ALA* 5.0 1.7 - - - +
169A PRO* 3.5 23.6 + - - +
170A VAL* 3.0 27.8 + - - +
171A PHE* 3.7 3.2 - - - +
203A GLU* 3.0 38.7 + - - +
204A ALA 3.2 6.0 + - - +
206A ASN* 1.3 76.5 - - + +
208A TYR* 1.3 53.1 + - - +
210A ALA* 3.7 4.6 - - - +
211A GLY* 2.7 32.4 + - - -
212A ASP 4.2 1.4 + - - -
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Residues in contact with TYR 208 (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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110A VAL* 3.9 22.4 - - + -
111A LEU* 3.7 31.2 - - + -
114A ALA* 3.2 31.0 - - + +
146A THR* 3.4 22.2 - - - -
149A PRO* 3.7 0.3 - - - +
150A LYS* 2.9 44.2 + - + +
151A GLY 2.8 32.2 + - - -
153A LEU* 3.6 22.2 - - + -
170A VAL* 4.3 8.7 - - + +
204A ALA 3.0 16.8 + - - +
205A GLU* 3.8 3.6 - - - +
207A ARG* 1.3 74.7 - - - +
209A ILE* 1.3 64.2 + - + +
211A GLY* 3.4 7.3 + - - -
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Residues in contact with ILE 209 (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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110A VAL* 4.3 20.4 - - + -
149A PRO* 3.2 20.8 - - - +
150A LYS* 4.2 30.5 - - - +
205A GLU* 3.0 41.0 + - + +
206A ASN* 3.9 9.0 - - - +
208A TYR* 1.3 77.0 - - + +
210A ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 210 (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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149A PRO* 3.7 11.2 - - - +
206A ASN 3.0 19.5 + - - +
207A ARG* 3.7 5.6 - - - +
209A ILE* 1.3 79.3 - - - +
211A GLY* 1.3 65.4 + - - +
212A ASP* 3.1 15.7 + - + +
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Residues in contact with GLY 211 (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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146A THR* 3.9 2.5 - - - -
148A GLY* 3.5 22.7 - - - -
149A PRO* 3.5 20.2 - - - +
168A ALA* 3.5 12.9 - - - +
207A ARG 2.7 19.9 + - - -
208A TYR 3.4 1.8 + - - -
209A ILE 3.3 2.8 - - - -
210A ALA* 1.3 74.3 - - - +
212A ASP* 1.3 58.5 + - - +
213A LYS* 3.6 7.1 + - - +
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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