Contacts of the strand formed by residues 241 - 246 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A THR* 3.7 33.2 - - + +
175A LEU* 4.0 15.3 - - + -
200A ILE* 4.3 3.1 - - + -
232A ILE* 3.8 22.4 - - + -
236A THR* 4.0 2.2 - - + -
240A GLY* 1.3 74.5 - - - -
242A ASP* 1.3 60.7 + - - +
243A ALA 3.7 7.6 - - - +
244A VAL* 3.6 31.9 - - + -
260A ALA* 2.8 26.4 + - + +
261A LEU* 3.5 5.2 - - + +
262A ALA* 2.8 21.5 + - - -
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA 4.8 1.2 - - - +
171A THR 4.1 0.2 - - - +
172A LYS* 3.1 45.9 + - + +
173A THR* 2.9 29.6 + - - +
239A LYS* 3.0 36.0 + - - +
240A GLY 4.8 0.9 - - - +
241A VAL* 1.3 73.7 - - - +
243A ALA* 1.3 62.4 + - + +
262A ALA* 4.2 6.1 - - - +
263A LYS 4.8 2.3 - - - +
264A GLN 4.3 1.7 - - - +
265A GLY* 3.2 8.3 - - - -
266A LYS* 3.0 23.9 + - - +
102B TYR* 4.7 3.5 - - - -
103B TYR* 4.4 2.9 + - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 3.7 38.1 - - + +
168A LEU* 3.8 13.9 - - + -
173A THR 3.3 3.2 + - - +
174A LEU* 3.4 6.2 - - + -
175A LEU 2.9 24.1 + - - -
241A VAL* 3.2 4.7 - - - +
242A ASP* 1.3 83.1 - - - +
244A VAL* 1.3 66.9 + - - +
261A LEU* 4.7 0.4 - - - -
266A LYS* 3.2 12.3 - - + +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 3.3 17.7 - - + +
177A VAL* 3.7 27.6 - - + -
241A VAL* 3.6 26.7 - - + -
243A ALA* 1.3 73.6 - - - +
245A ILE* 1.3 65.4 + - - +
246A ASP 4.0 0.2 - - - +
257A TYR* 4.5 5.4 - - + +
261A LEU* 3.7 14.4 - - + -
266A LYS 2.8 6.8 + - - +
267A TYR* 3.6 38.1 - - + -
268A VAL* 2.7 36.1 + - - +
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Residues in contact with ILE 245 (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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159A THR* 5.6 0.4 - - + -
162A ALA* 3.9 17.7 - - + +
163A VAL* 3.7 34.1 - - + +
166A ALA* 4.7 2.2 - - + -
174A LEU* 3.8 23.3 - - + -
175A LEU 2.9 10.8 + - - +
176A VAL* 3.6 6.1 - - + -
177A VAL 3.0 23.2 + - - +
187A ALA* 4.6 13.7 - - + -
244A VAL* 1.3 77.2 - - - +
246A ASP* 1.3 59.9 + - - +
247A LEU* 3.6 27.7 + - + +
268A VAL* 3.6 15.9 - - + -
270A VAL* 4.3 14.6 - - + -
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Residues in contact with ASP 246 (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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177A VAL* 3.9 13.2 - - + +
244A VAL* 3.8 1.5 - - + -
245A ILE* 1.3 70.4 - - - +
247A LEU* 1.3 60.5 + - - +
248A ASN* 2.6 35.3 + - - +
249A ASN* 2.8 29.1 + - - +
253A THR* 2.6 25.6 + - - -
254A LEU 4.3 0.2 + - - -
267A TYR* 2.6 34.8 + - + +
268A VAL 3.0 9.9 + - - +
270A VAL* 3.1 10.6 + - - -
271A 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