Contacts of the strand formed by residues 262 - 267 (chain A) in PDB entry 4M83
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 TRP 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ALA* 5.8 0.4 - - - -
232A LYS* 3.2 34.3 - - + +
234A VAL* 3.9 22.7 - - + -
256A PHE* 4.0 14.1 - + + +
259A LEU* 3.1 36.0 + - + +
260A PRO 3.6 15.3 - - - -
261A GLY* 1.3 82.6 - - - +
263A HIS* 1.3 61.2 + - - +
283A ASN* 2.8 30.5 + - - +
301A LEU* 3.7 21.5 - - + -
360A ALA* 3.8 15.0 - - + -
361A LEU* 3.7 30.1 - - + +
364A VAL* 3.6 41.5 - - + -
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Residues in contact with HIS 263 (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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224A TRP* 4.5 2.0 - + - -
227A PRO* 3.6 32.7 - - + +
230A ALA* 4.2 20.4 - - + -
232A LYS 2.9 7.3 + - - -
233A VAL* 3.3 8.7 - - + +
234A VAL* 2.9 27.9 + - - +
261A GLY 4.1 0.4 + - - -
262A TRP* 1.3 74.3 - - - +
264A LEU* 1.3 61.4 + - - +
265A VAL* 3.9 14.7 + - + -
282A ASP 4.9 2.9 - - - -
283A ASN* 3.4 28.6 + - - +
284A VAL 4.4 2.5 - - - -
285A GLU* 2.9 37.5 + - + +
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Residues in contact with LEU 264 (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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234A VAL* 3.4 29.6 - - + +
236A VAL* 3.9 21.1 - - + -
252A CYS 3.7 29.8 - - - +
253A VAL* 4.1 6.5 - - - -
256A PHE* 4.2 14.8 - - + +
262A TRP 4.2 0.6 - - - -
263A HIS* 1.3 73.3 + - - +
265A VAL* 1.3 71.7 + - - +
266A LEU* 4.1 17.7 - - + +
283A ASN* 3.0 13.1 + - - +
284A VAL* 3.4 23.9 - - + -
285A GLU* 2.8 28.6 + - - +
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Residues in contact with VAL 265 (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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224A TRP* 3.4 36.3 - - + -
233A VAL* 4.3 9.9 - - + -
234A VAL 2.9 10.5 + - - +
235A LEU* 3.4 17.2 - - + +
236A VAL 3.0 25.5 + - - -
263A HIS* 3.9 4.7 + - + -
264A LEU* 1.3 72.6 - - - +
266A LEU* 1.3 60.5 + - - +
285A GLU* 3.5 20.2 - - + +
287A HIS* 4.2 12.8 - - + -
290A VAL* 4.2 4.3 - - + -
295A ILE* 3.6 28.7 - - + -
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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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236A VAL* 3.6 36.3 - - + -
249A TYR* 4.0 21.1 - - + +
252A CYS* 4.0 12.6 - - + -
253A VAL* 3.4 32.8 - - + -
264A LEU* 3.7 14.1 + - + -
265A VAL* 1.3 76.0 - - - +
267A GLN* 1.3 69.8 + - - +
268A ILE* 6.2 0.7 - - + -
284A VAL* 4.3 7.4 - - + -
285A GLU 2.6 15.3 + - - +
286A VAL* 3.2 17.0 - - + -
287A HIS* 2.9 26.3 + - - +
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Residues in contact with GLN 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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235A LEU* 5.5 0.2 - - + -
236A VAL 3.3 19.0 + - - +
237A SER* 3.3 13.9 + - - +
238A LEU* 3.0 29.3 - - - +
239A GLY 3.8 13.6 + - - +
243A THR* 4.4 2.5 - - - +
249A TYR* 3.3 38.9 + - - -
266A LEU* 1.3 79.5 - - - +
268A ILE* 1.3 90.5 + - - +
287A HIS* 3.5 19.1 - - + +
288A ASP 3.7 7.8 - - - +
289A TRP* 4.8 2.7 - - - +
290A VAL* 4.7 10.1 - - + -
1401A UDP 4.2 10.7 + - - +
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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