Contacts of the strand formed by residues 241 - 246 (chain B) in PDB entry 1R37
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 241 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B THR* 3.7 32.5 - - + +
175B LEU* 4.0 15.3 - - + -
200B ILE* 4.3 3.6 - - + -
232B ILE* 3.8 23.1 - - + -
236B THR* 4.0 2.9 - - + -
240B GLY* 1.3 74.6 - - - -
242B ASP* 1.3 61.4 + - - +
243B ALA 3.4 6.5 + - - +
244B VAL* 3.5 32.8 - - + -
260B ALA* 2.8 26.8 + - + +
261B LEU* 3.4 5.3 - - - +
262B ALA* 2.8 23.4 + - - -
265B GLY* 4.3 0.3 - - - -
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Residues in contact with ASP 242 (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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102A TYR* 4.7 4.3 + - - -
103A TYR* 4.5 2.8 + - - -
166B ALA 4.7 1.7 - - - +
171B THR 4.2 0.2 - - - +
172B LYS* 3.3 43.3 + - + +
173B THR* 3.0 30.3 + - - +
239B LYS* 2.9 37.8 + - - +
240B GLY 4.7 0.9 - - - +
241B VAL* 1.3 73.0 - - - +
243B ALA* 1.3 61.9 + - + +
262B ALA* 4.2 5.5 - - - +
263B LYS 4.8 2.4 - - - +
264B GLN 4.3 2.4 - - - +
265B GLY* 3.3 10.9 - - - +
266B LYS* 3.0 22.0 + - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA* 3.7 25.4 - - + +
168B LEU* 3.7 27.8 - - + -
173B THR 3.3 3.4 + - - +
174B LEU* 3.5 5.7 - - + -
175B LEU 2.9 24.3 + - - -
241B VAL* 3.2 4.9 - - - +
242B ASP* 1.3 81.8 - - - +
244B VAL* 1.3 68.7 + - - +
261B LEU* 4.7 0.4 - - - -
266B LYS* 3.2 10.3 - - + +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 3.2 21.3 - - + +
177B VAL* 3.8 24.0 - - + -
241B VAL* 3.5 28.9 - - + -
243B ALA* 1.3 72.3 - - - +
245B ILE* 1.3 65.9 + - - +
246B ASP 4.0 0.4 - - - +
257B TYR* 4.5 4.3 - - + +
261B LEU* 3.7 14.8 - - + -
266B LYS 2.8 6.6 + - - +
267B TYR* 3.6 37.0 - - + -
268B VAL* 2.7 34.9 + - - +
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Residues in contact with ILE 245 (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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159B THR* 5.6 0.9 - - + -
162B ALA* 3.9 26.9 - - + +
163B VAL* 3.7 33.2 - - + +
166B ALA* 4.7 2.5 - - + -
174B LEU* 3.8 23.6 - - + -
175B LEU 2.9 11.0 + - - +
176B VAL* 3.6 6.1 - - + -
177B VAL 3.0 23.2 + - - +
187B ALA* 4.5 13.5 - - + -
244B VAL* 1.3 77.9 - - - +
246B ASP* 1.3 59.4 + - - +
247B LEU* 3.6 27.5 + - + +
268B VAL* 3.5 15.3 - - + +
270B VAL* 4.4 5.6 - - + -
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Residues in contact with ASP 246 (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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177B VAL* 4.0 11.9 - - + +
244B VAL* 3.8 1.4 - - + -
245B ILE* 1.3 70.9 - - - +
247B LEU* 1.3 59.6 + - - +
248B ASN* 2.6 35.3 + - - +
249B ASN* 2.7 23.3 + - - +
253B THR* 2.7 24.5 + - - -
254B LEU* 4.3 0.5 + - - +
267B TYR* 2.6 43.4 + - + +
268B VAL 3.0 10.5 + - - +
270B VAL* 3.1 10.2 + - - -
271B GLY 2.9 18.7 + - - -
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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