Contacts of the strand formed by residues 238 - 242 (chain B) in PDB entry 1A7A
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 ARG 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B GLY 5.5 0.2 - - - -
214B LYS 2.7 14.0 + - - +
215B VAL* 3.4 34.1 - - + +
216B ALA 3.1 19.5 + - - +
236B GLY 4.2 0.4 + - - -
237B ALA* 1.3 67.9 - - - +
239B VAL* 1.3 64.9 + - - +
240B ILE* 3.5 13.2 + - + +
258B GLU* 3.9 20.2 + - - +
268B GLU* 4.2 15.0 + - - +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ALA* 3.4 7.9 - - + +
218B VAL* 4.4 7.9 - - + -
229B ALA* 3.5 32.1 - - + +
232B LEU* 3.6 23.3 - - + -
233B ARG* 3.6 12.5 - - + +
237B ALA 3.4 5.9 + - - +
238B ARG* 1.3 74.7 - - - +
240B ILE* 1.3 66.3 + - - +
241B ILE* 3.9 17.9 - - + -
257B TYR* 3.5 42.8 - - + +
258B GLU* 3.9 6.1 + - - +
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Residues in contact with ILE 240 (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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215B VAL* 3.6 29.2 - - + -
216B ALA 2.7 9.7 + - - +
217B VAL* 3.2 7.7 - - + +
218B VAL 2.8 26.3 + - - -
238B ARG* 4.1 12.3 - - + +
239B VAL* 1.3 77.1 - - - +
241B ILE* 1.3 68.3 + - - +
242B THR* 5.6 0.4 - - + -
258B GLU* 3.5 32.8 - - + +
260B THR* 4.0 15.5 - - - +
265B ALA* 3.9 23.6 - - + -
268B GLU* 3.6 29.6 - - + +
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Residues in contact with ILE 241 (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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218B VAL* 3.4 15.5 - - + +
220B GLY 4.7 1.1 - - - +
221B TYR* 3.2 47.6 - - + -
229B ALA* 3.8 15.5 - - + -
239B VAL* 3.9 8.9 + - + -
240B ILE* 1.3 79.4 - - - +
242B THR* 1.3 78.0 + - - +
243B GLU* 4.5 2.9 - - + -
252B ALA* 4.1 15.5 - - + -
257B TYR* 3.8 19.3 - - + -
258B GLU 2.9 13.1 + - - +
259B VAL* 3.0 15.3 - - + +
260B THR 2.8 28.1 + - - -
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Residues in contact with THR 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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407A THR* 4.2 7.6 - - - -
217B VAL* 4.5 16.2 - - + -
218B VAL 3.2 4.0 + - - -
219B ALA* 2.8 32.3 - - + +
220B GLY* 2.7 27.0 + - - -
240B ILE* 5.6 0.2 - - + -
241B ILE* 1.3 77.5 - - - +
243B GLU* 1.3 65.8 + - - +
259B VAL* 4.7 0.2 - - - -
260B THR 3.2 20.4 - - - +
261B THR 3.8 2.5 - - - +
262B MSE 3.6 30.5 - - + +
265B ALA* 4.9 2.7 - - + -
281B ILE* 5.5 0.2 - - - +
434B NAD 3.8 7.0 - - - -
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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