Contacts of the strand formed by residues 168 - 174 (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 ALA 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.2 5.1 - - - -
146B THR* 3.0 42.1 + - + +
148B GLY 5.2 0.2 - - - +
167B ALA* 1.3 71.2 - - - +
169B PRO* 1.3 70.1 - - - +
170B VAL 3.6 0.3 + - - -
207B ARG 5.1 1.1 - - - +
211B GLY* 3.4 40.4 - - - +
212B ASP 3.6 13.7 - - - +
213B LYS* 3.8 3.2 - - + +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 6.3 0.2 - - + -
90B LEU* 4.2 29.4 - - + -
143B TRP* 4.3 16.6 - - + -
144B LEU 4.0 0.2 - - - +
145B VAL* 3.9 10.1 - - + -
164B VAL* 3.7 25.8 - - + +
167B ALA 3.6 6.5 - - - +
168B ALA* 1.3 85.6 - - + +
170B VAL* 1.3 61.2 + - - +
207B ARG* 3.5 24.0 - - - +
212B ASP 4.3 8.7 - - - +
213B LYS 4.7 4.0 - - - +
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Residues in contact with VAL 170 (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* 4.5 0.2 - - - +
111B LEU* 3.5 32.5 - - + -
144B LEU* 2.8 35.1 + - + +
145B VAL* 4.0 18.2 - - - -
146B THR* 4.1 15.0 - - + +
153B LEU* 4.4 1.3 - - + -
168B ALA 4.0 2.7 - - - +
169B PRO* 1.3 76.6 - - - +
171B PHE* 1.3 63.7 + - + +
204B ALA* 3.5 22.1 - - + +
207B ARG* 3.1 26.9 + - - -
208B TYR* 4.3 14.8 - - + -
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Residues in contact with PHE 171 (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* 3.2 23.6 - - + +
125B PHE* 3.8 10.3 - + - -
129B PHE* 3.6 39.7 - + - -
143B TRP* 3.6 7.7 - - - -
144B LEU* 3.1 60.1 + - + -
169B PRO 3.7 0.4 - - - -
170B VAL* 1.3 84.9 - - + +
172B GLY* 1.3 67.2 + - - +
173B VAL* 3.9 8.3 - - + -
196B TRP* 4.0 13.7 - + - -
199B ILE* 4.2 23.6 - - + -
201B TRP* 3.7 24.5 - + - -
204B ALA* 4.5 6.1 - - + -
207B ARG* 3.8 1.1 - - - +
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Residues in contact with GLY 172 (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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91B PHE* 3.3 15.7 - - - -
94B ASN* 2.8 26.3 - - - +
141B TRP* 4.6 2.5 - - - -
142B GLY 3.2 10.8 - - - -
143B TRP* 3.3 20.4 - - - -
171B PHE* 1.3 77.2 - - - +
173B VAL* 1.3 67.8 + - - +
199B ILE* 5.2 0.3 - - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 3.8 2.5 - - - -
129B PHE* 3.7 19.3 - - + -
133B LEU* 3.9 31.0 - - + +
141B TRP* 3.6 3.9 - - - -
142B GLY 2.9 28.1 + - - -
171B PHE* 3.9 10.3 - - + -
172B GLY* 1.3 79.0 - - - +
174B ASP* 1.3 74.0 + - - +
175B MET* 3.4 7.4 + - - -
191B TYR* 4.1 5.2 - - + +
192B ALA* 5.8 0.2 - - - -
195B ILE* 3.9 39.3 - - + -
196B TRP* 6.3 0.4 - - + -
199B ILE* 4.4 4.5 - - + -
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Residues in contact with ASP 174 (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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40B HIS* 2.8 6.6 + - - -
88B HIS* 3.2 2.8 + - - -
91B PHE* 3.6 21.4 - - + -
141B TRP* 3.4 30.8 - - + -
173B VAL* 1.3 70.5 - - - +
175B MET* 1.3 59.9 + - - +
176B TRP* 3.0 35.9 + - - +
179B ALA* 3.6 14.1 - - + +
191B TYR* 3.0 26.2 + - - -
2002B MN 1.9 37.4 + - - -
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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