Contacts of the strand formed by residues 262 - 267 (chain C) in PDB entry 2X06
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 ASP 262 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C GLY* 5.6 1.2 - - - -
110C ALA* 3.4 4.0 - - - -
111C THR* 2.2 63.4 + - - +
117C PHE* 3.5 18.6 - - + +
137C ILE 3.3 15.5 - - - +
138C THR* 3.5 7.6 - - - +
237C SER 3.2 9.1 + - - +
260C LYS* 2.7 28.5 + - - -
261C GLY* 1.3 73.2 - - - +
263C LEU* 1.3 61.1 + - - +
264C PHE* 3.7 20.8 - - + -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 3.5 24.7 - - + -
109C VAL 3.4 20.4 - - - +
110C ALA* 3.8 11.0 - - + +
135C ILE 3.7 1.4 - - - +
136C THR* 3.5 5.2 - - - +
137C ILE* 3.2 53.7 + - + +
236C LEU* 3.5 29.4 - - + +
237C SER* 4.1 0.6 + - - -
239C ILE* 4.2 15.3 - - + -
262C ASP* 1.3 74.9 - - - +
264C PHE* 1.3 66.8 + - - +
265C ILE* 4.1 23.3 - - + -
267D ILE* 4.8 8.7 - - + -
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Residues in contact with PHE 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY* 3.8 15.9 - - - -
93C ALA* 3.6 20.9 - - + -
94C MSE 4.0 26.7 - - + +
97C ALA* 4.0 3.1 - - + +
107C GLY 3.8 0.9 - - - +
108C VAL* 3.4 4.2 - - - +
109C VAL* 2.8 44.6 + - + +
111C THR* 3.3 25.4 - - + -
117C PHE* 3.6 25.8 - + - -
123C TYR* 3.7 24.7 - + + -
135C ILE 3.7 1.8 - - - -
136C THR* 3.5 32.8 - - + -
262C ASP* 3.7 11.9 - - + -
263C LEU* 1.3 74.1 - - - +
265C ILE* 1.3 64.2 + - - +
266C ALA 4.3 0.2 - - - -
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C MSE 3.6 6.0 - - - +
106C VAL* 4.5 2.5 - - + -
107C GLY 3.4 7.9 - - - +
108C VAL* 4.0 24.9 - - + -
133C ILE 3.7 0.3 - - - +
134C GLY* 3.3 4.5 - - - -
135C ILE* 2.7 62.7 + - + +
263C LEU* 4.1 21.3 - - + -
264C PHE* 1.3 82.6 - - - +
266C ALA* 1.3 63.7 + - - +
267C ILE* 3.9 27.6 - - + -
135D ILE* 6.1 2.7 - - + -
265D ILE* 6.6 0.2 - - + -
267D ILE* 4.6 11.4 - - + -
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Residues in contact with ALA 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C MSE 4.4 3.4 - - - -
97C ALA* 3.8 30.2 - - + +
98C ILE* 3.9 21.5 - - + +
101C ALA* 3.7 6.0 - - + +
106C VAL* 3.4 6.4 - - - +
107C GLY 2.9 32.4 + - - +
127C ALA* 4.6 2.7 - - + -
132C MSE 4.6 3.6 - - - -
133C ILE 3.3 6.5 - - - +
265C ILE* 1.3 72.8 - - - +
267C ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA* 4.6 0.2 - - - -
105C GLY 3.5 4.3 - - - +
106C VAL* 3.8 16.4 - - + -
132C MSE 3.3 4.2 - - - +
133C ILE* 2.9 46.8 + - + +
135C ILE* 4.9 8.1 - - + -
265C ILE* 3.9 15.5 - - + -
266C ALA* 1.3 79.9 - - - +
268C ASN* 1.3 62.2 + - - +
269C PRO* 3.4 4.9 - - + +
272C PHE* 3.8 26.9 - - + -
108D VAL* 4.9 12.6 - - + -
236D LEU* 4.8 19.7 - - + -
239D ILE* 4.4 13.0 - - + -
263D LEU* 4.9 6.7 - - + -
265D ILE* 5.0 8.7 - - + -
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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