Contacts of the strand formed by residues 265 - 268 (chain A) in PDB entry 1MRA
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 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN* 3.0 48.6 + - + +
237A SER* 6.0 0.6 - - - +
239A LEU 2.8 28.3 + - - -
240A ASN* 3.0 26.9 + - - +
241A VAL 4.6 1.0 + - - -
242A PRO* 4.1 16.1 - - + +
243A VAL 3.3 4.8 + - - -
264A CYS* 1.4 77.4 - - - +
266A LEU* 1.3 64.9 + - + +
291A GLY 4.7 1.6 - - - +
292A ILE* 3.7 16.8 - - - +
293A PRO* 3.8 14.4 - - - +
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Residues in contact with LEU 266 (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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219A TRP* 3.4 36.3 - - + -
242A PRO* 3.5 34.1 - - + -
243A VAL 3.3 3.8 + - - +
244A GLN* 2.9 23.6 + - + +
245A MET 3.3 7.6 + - - -
264A CYS* 3.2 19.5 - - - +
265A ARG* 1.3 87.1 - - + +
267A ALA* 1.3 62.8 + - - +
292A ILE* 3.9 3.8 - - - -
293A PRO* 3.8 30.3 - - + +
314A HIS* 3.9 19.3 - - + +
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Residues in contact with ALA 267 (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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244A GLN* 2.8 8.9 + - - +
245A MET 3.0 10.8 - - - +
249A TRP* 3.8 24.0 - - + -
255A MET* 5.0 6.7 - - + -
259A LEU* 5.3 0.7 - - + -
264A CYS* 4.9 0.4 - - - -
266A LEU* 1.3 75.9 - - - +
268A MET* 1.3 58.9 - - - +
269A PRO* 3.8 7.4 - - + -
292A ILE* 3.8 16.1 - - + +
293A PRO 3.3 6.3 + - - +
294A MET* 3.4 7.6 - - + -
295A SER* 2.8 24.1 + - - -
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Residues in contact with MET 268 (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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137A TYR* 4.1 10.3 - - - +
164A LYS* 4.2 1.6 - - - +
219A TRP* 4.3 5.2 - - - -
221A GLU* 3.2 41.7 - - - +
244A GLN* 3.4 27.8 - - + +
245A MET 3.0 13.3 + - - +
246A GLY 3.4 14.0 - - - +
247A GLU* 3.5 9.0 + - + +
267A ALA* 1.3 75.7 - - - +
269A PRO* 1.3 72.4 - - - +
295A SER* 3.1 20.6 - - - +
296A SER 3.6 9.9 - - - +
297A HIS* 3.6 38.2 - - + +
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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