Contacts of the strand formed by residues 175 - 178 (chain B) in PDB entry 4KPF
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LEU* 4.4 3.8 - - - -
169B GLY 3.4 14.8 - - - +
170B ILE* 4.0 13.9 - - + +
171B SER 4.3 3.6 - - - +
174B TYR* 1.3 75.1 - - - +
176B THR* 1.3 62.4 - - - +
177B ASP* 5.6 1.3 - - - +
328B ASN* 3.3 23.6 + - - +
330B VAL* 3.3 20.7 - - - +
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 4.4 0.7 - - - +
30B LEU* 3.9 13.5 - - + -
31B PRO* 4.0 12.3 - - + -
167B SER* 4.3 2.2 - - - -
168B THR* 3.0 26.4 - - - +
169B GLY* 3.0 28.7 + - - -
175B ALA* 1.3 79.7 - - - +
177B ASP* 1.3 71.4 + - - +
178B ILE* 3.9 8.5 - - - +
328B ASN* 3.4 4.5 - - - +
330B VAL* 2.6 40.0 + - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER 3.7 3.8 - - - -
168B THR* 3.7 16.9 + - - -
169B GLY 4.2 5.2 - - - +
175B ALA* 5.6 0.9 - - - +
176B THR* 1.3 86.6 + - - +
178B ILE* 1.3 59.7 + - - +
262B GLU* 3.8 18.2 - - - +
325B TYR* 3.4 16.4 + - + +
326B ASN 3.8 16.4 - - - +
327B PHE* 3.9 2.9 - - - -
328B ASN* 2.9 40.7 + - + +
329B MET* 3.6 2.4 + - - +
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Residues in contact with ILE 178 (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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31B PRO* 4.9 0.4 - - + -
162B LEU* 3.3 53.8 - - + +
163B LEU* 4.7 9.2 - - + -
166B GLY* 3.1 4.6 - - - -
167B SER* 3.0 37.6 + - - +
168B THR* 5.2 0.2 - - - +
176B THR* 3.9 5.6 - - - +
177B ASP* 1.3 77.9 - - - +
179B PRO* 1.3 78.1 - - + +
180B PRO* 4.2 1.4 - - - +
261B TYR* 5.5 2.6 + - - -
325B TYR* 3.2 3.8 + - - -
329B MET* 3.7 32.8 - - + -
330B VAL 4.1 18.2 - - - +
331B ALA* 5.0 0.2 - - + -
340B VAL* 5.9 0.4 - - + -
345B ILE* 5.1 2.7 - - + -
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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