Contacts of the strand formed by residues 234 - 238 (chain A) in PDB entry 2PI8
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 VAL 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR 4.5 0.7 + - - +
160A ASP* 2.9 44.5 + - - +
163A GLY 4.7 0.2 - - - +
180A TYR* 3.7 32.8 - - + -
182A GLY 3.4 11.0 - - - +
183A LYS* 4.1 14.4 - - + -
232A SER* 5.2 1.6 - - - +
233A PHE* 1.3 91.0 - - - +
235A PHE* 1.3 73.5 + - - +
236A PHE* 3.6 33.6 - - + -
3E NAG 5.9 0.7 - - + +
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR* 3.7 12.3 - - + -
122A ARG 3.3 28.0 - - - -
123A MSE 3.9 15.9 - - + +
124A PRO* 3.8 17.5 - - + -
128A GLY 4.8 0.7 - - - -
129A ARG* 3.9 18.2 - - + -
136A ILE* 4.2 7.4 - - + -
141A LEU* 3.6 26.9 - - + -
181A ALA* 3.0 21.7 + - - -
182A GLY 2.9 14.3 + - - +
183A LYS* 3.8 33.4 - - - -
184A ASN* 3.8 10.8 - - + -
233A PHE* 3.6 26.0 - + - -
234A VAL* 1.3 78.3 - - - +
236A PHE* 1.3 61.7 + - - +
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Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 3.8 20.9 - - + -
121A TYR 3.2 11.6 + - - +
122A ARG* 3.4 26.0 - - - +
123A MSE 3.9 0.7 + - - -
147A LEU* 3.8 3.3 - - + +
156A ASN 5.4 0.7 - - - -
159A MSE 3.6 33.9 - - + -
160A ASP* 4.0 17.3 - - - -
163A GLY 3.6 27.4 - - - -
164A SER* 4.0 5.6 - - - -
178A PHE* 3.4 39.5 - + + -
179A SER 3.2 11.2 - - - +
181A ALA* 3.6 6.0 - - - +
233A PHE* 6.4 0.4 - + - -
234A VAL* 3.6 31.9 - - + -
235A PHE* 1.3 76.5 - - - +
237A LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 5.7 0.2 - - - -
178A PHE* 4.2 1.3 - - - -
179A SER* 2.9 39.5 + - - +
181A ALA* 3.7 15.9 - - + -
236A PHE* 1.3 75.5 - - - +
238A PRO* 1.3 74.8 - - + +
239A GLN* 3.3 9.8 + - - +
699A PO4 2.8 34.1 + - - +
698D PO4 2.9 33.8 + - - -
6E NAG 3.9 11.0 + - + +
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Residues in contact with PRO 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 5.4 1.6 - - + -
147A LEU* 3.8 33.0 - - + -
176A ASN* 3.2 28.0 - - - +
177A PHE 3.5 2.7 - - - +
178A PHE* 3.7 19.7 - - + -
236A PHE 4.2 0.4 - - - +
237A LYS* 1.3 92.7 - - + +
239A GLN* 1.3 62.0 + - - +
240A SER* 3.3 4.0 - - - -
245D LYS* 5.9 0.9 + - - -
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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