Contacts of the strand formed by residues 231 - 235 (chain I) in PDB entry 2X86
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 GLY 231 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151I VAL* 5.9 0.2 - - - -
155I LEU* 4.2 17.8 - - - +
162I ILE* 2.9 10.9 + - - +
163I VAL* 3.2 7.5 - - - +
164I GLY 2.9 23.6 + - - -
230I SER* 1.3 75.5 - - - +
232I ILE* 1.3 64.7 + - - +
233I PHE* 3.5 10.2 - - - -
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Residues in contact with ILE 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I TYR* 3.6 23.3 - - - +
115I SER* 5.1 0.9 - - - +
129I GLU* 3.4 27.0 - - + +
148I ASP* 3.8 34.8 - - + +
151I VAL* 4.4 9.9 - - + -
152I ARG* 3.9 25.1 - - + +
155I LEU* 5.1 3.1 - - + +
164I GLY 3.4 11.0 - - - +
166I ARG* 4.1 32.8 - - + +
231I GLY* 1.3 76.5 - - - +
233I PHE* 1.3 70.3 + - - +
282I ASN* 5.0 2.1 + - - +
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Residues in contact with PHE 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I GLU* 3.4 2.5 - - - +
163I VAL* 4.0 8.7 - - + -
164I GLY 2.9 10.6 + - - +
165I PHE* 3.5 10.7 - - + -
166I ARG* 2.7 33.2 + - - -
224I PHE* 3.6 26.0 - + - -
229I VAL* 4.5 2.5 - - + -
230I SER 3.4 21.3 - - - -
231I GLY* 3.5 26.7 - - - -
232I ILE* 1.3 80.8 - - - +
234I ASN* 1.3 65.0 + - - +
282I ASN* 3.7 23.6 - - + -
283I LEU* 3.8 32.3 - - + -
286I ALA* 3.8 19.3 - - + -
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Residues in contact with ASN 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I TYR* 2.6 29.2 + - - -
127I PHE 2.7 27.6 + - - -
129I GLU* 2.7 26.4 + - - +
166I ARG* 3.7 9.3 - - - -
168I PHE* 3.6 17.0 - - + -
233I PHE* 1.3 77.3 - - - +
235I LEU* 1.3 59.8 - - - +
236I GLY 4.0 0.7 - - - -
278I ALA* 4.1 6.3 - - + -
279I ASP 2.8 27.3 + - - +
280I LEU* 4.2 3.1 - - + +
283I LEU* 3.7 21.5 - - + +
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I PHE* 4.1 9.9 - - + -
166I ARG 2.9 12.4 + - - +
167I TYR* 3.5 38.1 - - + -
168I PHE* 3.1 28.0 + - - -
212I VAL* 3.9 7.9 - - + +
217I VAL* 4.1 26.2 - - + +
220I VAL* 3.7 37.9 - - + -
221I ASN* 4.7 0.4 - - - +
233I PHE 4.4 3.4 - - - +
234I ASN* 1.3 74.2 - - - +
236I GLY* 1.3 60.1 + - - +
283I LEU* 5.0 3.6 - - + -
292I PHE* 3.8 26.2 - - + -
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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