Contacts of the helix formed by residues 200 - 211 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS 3.2 15.0 + - - +
94B ASN* 3.0 30.0 + - - +
95B LEU 3.5 16.0 + - - +
96B ALA* 3.8 16.3 - - + +
100B SER 5.5 1.8 - - - +
101B GLY 4.8 4.5 - - - +
198B VAL 3.4 2.0 + - - -
199B ILE* 1.3 71.8 - - - +
201B TRP* 1.3 61.1 + - - +
202B ALA* 3.3 13.4 + - - +
203B GLU* 3.1 29.8 + - - +
204B ALA* 3.2 10.7 + - - +
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Residues in contact with TRP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 4.5 4.0 + - - +
103B GLY* 3.7 7.5 + - - -
104B LYS 3.5 22.7 - - - +
105B ILE* 3.4 45.0 - - + +
108B ALA* 3.4 14.5 - - + +
111B LEU* 3.9 20.9 - - + -
115B ILE* 4.2 6.3 - - + -
122B PHE* 3.6 32.0 - + - -
125B PHE* 4.3 4.0 - + - -
171B PHE* 3.7 33.0 - + - -
196B TRP* 4.0 18.0 + + - -
199B ILE* 3.0 42.5 + - + +
200B ASN* 1.3 69.2 - - - +
202B ALA* 1.3 59.7 + - - +
204B ALA* 3.5 13.8 - - + +
205B GLU* 2.8 31.0 + - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 5.5 0.2 + - - -
107B GLN* 4.0 34.7 + - + +
200B ASN* 3.2 10.6 + - - +
201B TRP* 1.3 78.0 - - - +
203B GLU* 1.3 61.0 - - - +
205B GLU* 3.5 4.1 - - - +
206B ASN* 3.3 27.1 + - - +
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LYS* 3.4 42.4 + - - +
94B ASN* 4.3 2.0 - - - -
200B ASN* 3.1 21.0 + - - +
202B ALA* 1.3 76.0 - - - +
204B ALA* 1.3 64.2 + - - +
206B ASN* 3.2 14.5 + - - +
207B ARG* 3.0 62.0 + - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASN* 5.4 0.8 - - - +
111B LEU* 3.4 22.0 - - + -
170B VAL* 3.5 29.0 - - + +
171B PHE* 4.5 8.3 - - + -
199B ILE* 5.6 0.2 - - + -
200B ASN 3.2 10.4 + - - +
201B TRP* 3.1 23.2 + - + +
203B GLU* 1.3 75.9 - - - +
205B GLU* 1.3 57.2 + - - +
207B ARG* 3.2 1.6 + - - +
208B TYR* 2.8 31.4 + - - +
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLN 4.3 4.3 - - - +
108B ALA* 3.3 19.2 - - + -
109B PRO* 3.1 11.8 - - + +
110B VAL* 2.8 36.0 + - - +
111B LEU* 2.6 38.8 + - - +
201B TRP 2.8 16.8 + - - +
202B ALA* 3.5 7.6 - - - +
204B ALA* 1.3 77.7 - - - +
206B ASN* 1.3 67.1 + - - +
208B TYR* 3.3 1.6 + - - +
209B ILE* 3.0 41.5 + - + +
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ALA 3.3 13.4 + - - +
203B GLU* 3.2 20.8 + - - +
205B GLU* 1.3 83.6 - - - +
207B ARG* 1.3 59.9 + - + +
209B ILE* 3.4 8.9 + - - +
210B ALA* 2.9 32.2 + - - +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 2.9 53.3 + - - +
93B LYS* 3.5 21.4 - - - +
94B ASN* 3.1 27.5 - - - +
143B TRP* 5.6 0.4 - - - -
146B THR* 4.8 1.0 - - - +
168B ALA* 5.1 1.0 - - - +
169B PRO* 3.5 24.1 + - - +
170B VAL* 3.1 26.4 + - - +
171B PHE* 3.8 1.0 - - - +
203B GLU* 3.0 37.6 + - - +
204B ALA 3.6 5.4 - - - +
206B ASN* 1.3 75.9 - - + +
208B TYR* 1.3 54.2 + - - +
210B ALA* 3.8 4.4 - - - +
211B GLY* 2.6 34.5 + - - -
212B ASP 4.3 1.4 + - - +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.8 22.9 - - + -
111B LEU* 3.7 30.5 - - + -
114B ALA* 3.4 28.7 - - + +
146B THR* 3.3 31.6 - - - -
148B GLY 3.9 0.3 - - - +
149B PRO* 3.6 0.5 - - - +
150B LYS* 2.9 44.1 + - - +
151B GLY 2.7 24.6 + - - -
153B LEU* 3.6 18.2 - - + -
170B VAL* 4.3 9.4 - - + +
204B ALA 2.8 17.2 + - - +
205B GLU 3.7 3.1 - - - +
207B ARG* 1.3 79.4 - - - +
209B ILE* 1.3 63.0 + - + +
211B GLY* 3.3 5.9 + - - -
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 4.1 21.5 - - + -
149B PRO* 3.0 24.1 - - - +
150B LYS* 3.9 30.9 - - + +
205B GLU* 3.0 39.5 + - + +
206B ASN* 3.9 9.6 - - - +
208B TYR* 1.3 76.3 - - + +
210B ALA* 1.3 58.0 + - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 3.6 12.2 - - - +
206B ASN 2.9 19.8 + - - +
207B ARG* 3.8 5.2 - - - +
209B ILE* 1.3 78.8 - - - +
211B GLY* 1.3 65.7 + - - +
212B ASP* 3.1 14.2 + - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B THR* 4.1 1.6 - - - -
148B GLY* 3.8 10.1 - - - -
149B PRO* 3.7 25.0 - - - +
168B ALA* 3.4 17.8 - - - +
207B ARG 2.6 21.0 + - - -
208B TYR 3.3 4.5 + - - -
210B ALA* 1.3 73.1 - - - +
212B ASP* 1.3 58.7 + - - +
213B LYS* 3.1 11.8 + - - +
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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