Contacts of the strand formed by residues 168 - 174 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145Y VAL* 3.2 4.6 - - - -
146Y THR* 2.9 54.5 + - + +
148Y GLY 5.2 0.4 - - - +
167Y ALA* 1.3 72.9 - - - +
169Y PRO* 1.3 70.3 - - + +
170Y VAL 3.5 0.3 + - - -
207Y ARG 5.1 1.6 - - - +
211Y GLY* 3.7 4.3 - - - -
212Y ASP 3.4 38.8 - - - +
213Y LYS* 3.9 3.5 - - + +
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Residues in contact with PRO 169 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y ILE* 6.3 0.2 - - + -
90Y LEU* 4.0 33.4 - - + +
143Y TRP* 4.4 15.5 - - + -
144Y LEU 4.2 3.4 - - - +
145Y VAL* 4.2 6.3 - - + -
164Y VAL* 3.7 26.0 - - + +
167Y ALA 3.5 6.7 - - - +
168Y ALA* 1.3 86.4 - - + +
170Y VAL* 1.3 61.5 + - - +
207Y ARG* 3.4 24.8 - - - +
212Y ASP 4.3 7.4 - - - +
213Y LYS 4.8 4.0 - - - +
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Residues in contact with VAL 170 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Y LEU* 3.6 24.2 - - + -
144Y LEU* 2.8 34.6 + - + +
145Y VAL 4.0 17.0 - - - -
146Y THR* 4.2 9.4 - - + +
153Y LEU* 4.3 14.6 - - + -
168Y ALA 4.0 2.5 - - - +
169Y PRO* 1.3 75.9 - - - +
171Y PHE* 1.3 62.1 + - + +
204Y ALA* 3.5 32.4 - - + +
207Y ARG* 3.1 28.4 + - - -
208Y TYR* 4.3 8.5 - - + -
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Residues in contact with PHE 171 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Y ASN* 3.4 22.4 - - + +
125Y PHE* 3.7 4.5 - + - -
129Y PHE* 3.6 29.6 - + - -
143Y TRP* 3.6 9.0 - - - -
144Y LEU* 3.1 60.3 + - + +
169Y PRO 3.7 0.4 - - - -
170Y VAL* 1.3 85.3 - - + +
172Y GLY* 1.3 67.6 + - - +
173Y VAL* 4.0 7.4 - - + -
196Y TRP* 3.5 32.3 - + - -
199Y ILE* 4.1 20.6 - - + -
201Y TRP* 3.6 25.4 - + - -
204Y ALA* 4.4 7.0 - - + -
207Y ARG* 3.9 1.6 - - - +
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Residues in contact with GLY 172 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y PHE* 3.4 13.9 - - - -
94Y ASN* 2.9 27.0 - - - +
141Y TRP* 4.5 2.5 - - - -
142Y GLY 3.3 10.8 - - - -
143Y TRP* 3.4 20.5 - - - -
171Y PHE* 1.3 77.7 - - - +
173Y VAL* 1.3 68.3 + - - +
199Y ILE* 5.0 0.5 - - - +
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Residues in contact with VAL 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Y PHE* 3.8 3.6 - - - -
129Y PHE* 3.7 19.5 - - + -
133Y LEU* 3.8 31.6 - - + +
141Y TRP* 3.5 5.5 - - - -
142Y GLY 2.9 28.7 + - - -
171Y PHE* 4.0 11.2 - - + -
172Y GLY* 1.3 78.3 - - - +
174Y ASP* 1.3 71.4 + - - +
175Y MET* 3.4 8.0 + - - -
191Y TYR* 4.1 12.3 - - + +
192Y ALA* 5.9 0.4 - - - -
195Y ILE* 4.2 29.6 - - + -
196Y TRP* 5.9 1.1 - - + -
199Y ILE* 4.5 4.3 - - + -
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Residues in contact with ASP 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y HIS* 2.8 9.2 - - - -
88Y HIS* 3.5 1.0 + - - -
91Y PHE* 3.6 21.1 - - + -
141Y TRP* 3.5 31.4 - - + -
173Y VAL* 1.3 72.7 - - - +
175Y MET* 1.3 59.8 + - - +
176Y TRP* 3.1 29.9 + - - -
178Y HIS* 3.6 0.2 + - - -
179Y ALA* 3.7 12.6 - - + +
191Y TYR* 2.9 28.4 + - - -
2004Y MN 2.0 35.0 + - - -
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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