Contacts of the helix formed by residues 200 - 211 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93X LYS 3.2 16.0 + - - +
94X ASN* 2.8 31.7 + - - +
95X LEU 3.5 15.3 + - - +
96X ALA* 3.7 16.1 - - + +
100X SER 4.7 5.8 + - - +
101X GLY 4.5 3.8 - - - +
198X VAL 3.4 1.2 + - - -
199X ILE* 1.3 71.9 - - - +
201X TRP* 1.3 60.3 + - - +
202X ALA* 3.3 19.8 + - - +
203X GLU* 3.3 14.9 + - - +
204X ALA* 3.2 17.0 + - - +
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Residues in contact with TRP 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X GLY 4.3 3.4 + - - +
103X GLY* 3.7 14.7 + - - -
104X LYS 3.7 15.5 - - - +
105X ILE* 3.4 44.2 - - + +
107X GLN 4.8 0.2 - - - -
108X ALA* 3.4 18.3 - - + +
111X LEU* 3.8 20.6 - - + -
115X ILE* 4.3 5.4 - - + -
122X PHE* 3.6 30.8 - + - -
125X PHE* 4.2 4.7 - + - -
171X PHE* 3.7 34.1 - + - -
196X TRP* 3.8 21.9 + + - -
199X ILE* 3.1 32.2 + - + +
200X ASN* 1.3 69.5 + - - +
202X ALA* 1.3 61.3 + - - +
203X GLU 3.1 0.2 - - - -
204X ALA* 3.5 14.5 - - + +
205X GLU 2.8 26.2 + - - -
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Residues in contact with ALA 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X GLY* 5.2 0.6 + - - -
107X GLN* 3.8 36.5 + - + +
200X ASN* 3.3 10.0 + - - +
201X TRP* 1.3 79.0 - - - +
203X GLU* 1.3 63.0 + - - +
205X GLU* 3.3 4.6 - - - +
206X ASN* 3.2 26.1 + - - +
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Residues in contact with GLU 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X LYS* 3.4 40.5 - - - +
94X ASN* 4.3 2.0 - - - -
200X ASN* 3.2 17.5 + - - +
201X TRP 3.1 0.2 - - - -
202X ALA* 1.3 77.5 - - - +
204X ALA* 1.3 65.7 + - - +
206X ASN* 3.2 15.1 + - - +
207X ARG* 3.0 65.1 + - - +
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Residues in contact with ALA 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X ASN* 5.4 0.6 - - - +
111X LEU* 3.5 22.0 - - + -
170X VAL* 3.6 28.1 - - + +
171X PHE* 4.6 7.2 - - + -
199X ILE* 5.5 0.2 - - + -
200X ASN 3.2 5.9 + - - +
201X TRP* 3.1 26.1 + - + +
203X GLU* 1.3 77.7 - - - +
205X GLU* 1.3 64.5 + - - +
207X ARG* 3.2 1.4 + - - -
208X TYR* 2.9 24.8 + - - +
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Residues in contact with GLU 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X GLN 4.2 5.8 - - - +
108X ALA* 3.4 19.6 - - + -
109X PRO* 3.1 11.2 - - + +
110X VAL* 2.9 35.4 + - - +
111X LEU* 2.8 33.9 + - - +
201X TRP 2.8 12.4 + - - +
202X ALA 3.3 11.4 - - - +
203X GLU 3.2 0.2 - - - -
204X ALA* 1.3 77.6 - - - +
206X ASN* 1.3 66.6 + - - +
208X TYR* 3.4 2.1 + - - +
209X ILE* 3.0 41.7 + - + +
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Residues in contact with ASN 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X ALA 3.2 14.4 + - - +
203X GLU* 3.2 19.6 + - - +
205X GLU* 1.3 86.5 - - - +
207X ARG* 1.3 56.9 + - + +
209X ILE* 3.4 10.1 + - - +
210X ALA* 2.9 31.2 + - - +
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Residues in contact with ARG 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X LEU* 2.8 53.0 + - - +
93X LYS* 3.6 21.2 - - - +
94X ASN* 2.9 29.1 - - - +
143X TRP* 5.7 0.2 - - - -
146X THR* 4.8 1.2 - - - +
168X ALA* 5.0 2.4 - - - +
169X PRO* 3.4 24.8 + - - +
170X VAL* 3.1 26.0 + - - +
171X PHE* 3.8 2.6 - - - +
203X GLU* 3.0 42.4 + - - +
204X ALA 3.7 4.9 - - - +
206X ASN* 1.3 75.3 - - + +
208X TYR* 1.3 55.0 + - - +
210X ALA* 3.8 5.1 - - - +
211X GLY* 2.6 33.1 + - - -
212X ASP 4.4 1.2 + - - -
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Residues in contact with TYR 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X VAL* 3.7 22.7 - - + -
111X LEU* 3.6 31.2 - - + -
114X ALA* 3.3 28.1 - - + +
146X THR* 3.4 21.7 - - + +
148X GLY 3.9 0.5 - - - +
149X PRO* 3.6 0.3 - - - +
150X LYS* 2.9 43.6 + - + -
151X GLY 2.6 31.5 + - - -
153X LEU* 3.5 24.9 - - + -
170X VAL* 4.3 8.9 - - + +
204X ALA 2.9 17.0 + - - +
205X GLU 3.7 3.8 - - - +
207X ARG* 1.3 77.8 - - - +
209X ILE* 1.3 62.1 + - + +
211X GLY* 3.4 8.3 + - - -
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Residues in contact with ILE 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X VAL* 4.3 21.1 - - + -
149X PRO* 3.0 26.0 - - - +
150X LYS* 3.8 28.5 + - + +
205X GLU* 3.0 41.2 + - + +
206X ASN* 3.9 9.4 - - - +
208X TYR* 1.3 75.3 - - + +
210X ALA* 1.3 58.4 + - - +
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Residues in contact with ALA 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X PRO* 3.5 11.3 - - - +
206X ASN 2.9 17.3 + - - +
207X ARG* 3.8 5.8 - - - +
209X ILE* 1.3 80.4 - - - +
211X GLY* 1.3 66.5 + - - +
212X ASP* 3.3 27.7 + - + +
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Residues in contact with GLY 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X THR* 4.1 1.8 - - - -
148X GLY* 3.6 21.1 - - - -
149X PRO* 3.6 19.0 - - - +
168X ALA* 3.5 12.6 - - - +
207X ARG 2.6 21.2 + - - -
208X TYR 3.4 4.0 + - - -
210X ALA* 1.3 74.1 - - - +
212X ASP* 1.3 60.8 + - - +
213X LYS* 3.5 5.9 + - - +
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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