Contacts of the strand formed by residues 168 - 174 (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 ALA 168 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145X VAL* 3.3 4.4 - - - -
146X THR* 2.9 42.6 + - + +
148X GLY 5.3 0.2 - - - +
167X ALA* 1.3 72.7 - - - +
169X PRO* 1.3 68.8 - - - +
170X VAL 3.4 0.5 + - - -
207X ARG 5.0 1.6 - - - +
211X GLY* 3.5 24.2 - - - +
212X ASP 3.4 29.6 - - - +
213X LYS* 3.7 2.2 - - + +
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Residues in contact with PRO 169 (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* 4.1 30.9 - - + +
143X TRP* 4.1 16.6 - - + -
144X LEU 4.0 4.9 - - - +
145X VAL* 4.2 5.4 - - + -
164X VAL* 3.6 26.0 - - + +
167X ALA 3.6 7.9 - - - +
168X ALA* 1.3 83.8 - - + +
170X VAL* 1.3 59.9 + - - +
171X PHE 5.0 0.4 - - - +
207X ARG* 3.4 24.8 - - - +
212X ASP 4.3 1.8 - - - +
214X GLY 4.0 23.1 - - - +
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Residues in contact with VAL 170 (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* 4.6 0.2 - - - +
111X LEU* 3.6 27.1 - - + -
144X LEU* 2.8 32.3 + - + +
145X VAL* 4.1 9.2 - - - -
146X THR* 4.1 15.9 - - + -
153X LEU* 4.4 1.3 - - + -
168X ALA 3.9 8.7 - - - +
169X PRO* 1.3 76.2 - - - +
171X PHE* 1.3 65.4 + - + +
204X ALA* 3.6 30.1 - - + +
207X ARG* 3.1 26.9 + - - -
208X TYR* 4.3 16.4 - - + +
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Residues in contact with PHE 171 (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* 3.3 23.6 - - + +
125X PHE* 3.8 4.0 - + - -
129X PHE* 3.7 31.6 - + - -
143X TRP* 3.5 9.0 - - - -
144X LEU* 3.1 61.6 + - + +
169X PRO 3.7 0.8 - - - -
170X VAL* 1.3 84.7 - - + +
172X GLY* 1.3 67.4 + - - +
173X VAL* 4.0 9.2 - - + -
196X TRP* 3.6 27.8 - + - -
199X ILE* 4.2 23.3 - - + -
201X TRP* 3.7 23.8 - + - -
204X ALA* 4.6 5.6 - - + -
207X ARG* 3.8 1.3 - - - +
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Residues in contact with GLY 172 (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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91X PHE* 3.3 22.2 - - - -
94X ASN* 3.0 18.7 - - - +
141X TRP* 4.3 1.8 - - - -
142X GLY 3.1 10.3 - - - -
143X TRP* 3.3 22.0 - - - -
171X PHE* 1.3 76.9 - - - +
173X VAL* 1.3 67.7 + - - +
199X ILE* 5.3 0.5 - - - +
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Residues in contact with VAL 173 (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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91X PHE* 3.8 2.9 - - - -
129X PHE* 3.8 20.4 - - + -
133X LEU* 3.9 28.5 - - + -
141X TRP* 3.6 4.8 - - - -
142X GLY 2.8 30.4 + - - -
171X PHE* 4.0 11.2 - - + -
172X GLY* 1.3 79.2 - - - +
174X ASP* 1.3 73.1 + - - +
175X MET* 3.4 2.8 + - - +
191X TYR* 4.0 17.5 - - + +
192X ALA* 5.7 0.4 - - - -
195X ILE* 4.0 33.2 - - + -
196X TRP* 5.8 0.7 - - + -
199X ILE* 4.4 3.8 - - + -
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Residues in contact with ASP 174 (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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40X HIS* 2.7 9.0 + - - -
88X HIS* 3.4 1.7 + - - -
91X PHE* 3.6 18.7 - - + -
141X TRP* 3.5 31.2 - - + -
173X VAL* 1.3 72.2 - - - +
175X MET* 1.3 63.3 + - - +
176X TRP* 3.1 25.9 + - - -
179X ALA* 3.6 16.9 - - + +
191X TYR* 3.0 25.5 + - - -
2003X MN 2.0 35.2 + - - -
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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