Contacts of the strand formed by residues 275 - 278 (chain H) in PDB entry 3MQ6
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 PHE 275 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H PRO* 4.1 20.0 - - + -
238H ALA* 3.3 20.2 - - + -
239H VAL 4.5 0.7 - - - -
240H ALA* 4.0 10.3 - - + -
252H GLN* 5.9 0.4 - - - -
253H PRO* 3.6 28.3 - - + -
256H GLU* 4.4 6.5 - - + -
257H ALA* 3.4 41.1 - - + -
260H MET* 3.8 19.3 - - + -
261H GLN* 5.0 0.2 - - - +
273H VAL* 3.7 8.9 + - + +
274H GLU* 1.3 74.8 - - - +
276H GLU* 1.3 74.0 + - - +
309H ALA 4.0 6.0 + - - +
310H ILE* 3.3 26.8 - - + -
311H ARG* 2.8 33.0 + - - +
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Residues in contact with GLU 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H MET* 5.9 0.5 - - - +
237H LEU* 3.9 17.9 - - + +
238H ALA 2.9 8.8 + - - +
239H VAL* 3.3 24.5 - - + +
240H ALA 3.0 23.2 + - - -
275H PHE* 1.3 78.7 - - - +
277H VAL* 1.3 64.4 + - - +
278H HIS* 2.8 20.1 + - + +
310H ILE* 4.4 0.4 - - - -
311H ARG* 2.9 26.3 + - + -
312H GLU 3.5 15.5 - - - +
314H TYR* 5.7 0.2 - - + -
325H ARG* 2.4 47.6 + - - +
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Residues in contact with VAL 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H ALA* 3.3 11.7 - - + +
242H LYS* 4.7 14.6 - - + -
245H LEU* 4.9 4.3 - - + -
253H PRO* 3.9 19.1 - - + -
276H GLU* 1.3 78.1 - - - +
278H HIS* 1.3 73.6 + - - +
291H TYR* 3.9 24.9 - - + +
310H ILE* 3.8 24.2 - - + -
312H GLU 3.1 6.7 + - - +
313H LEU* 3.5 23.1 - - + +
314H TYR 2.8 27.2 + - - +
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Residues in contact with HIS 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H PHE* 3.6 10.0 - - + -
106H SER* 5.3 0.4 + - - -
110H MET* 4.8 7.9 - - + -
239H VAL* 3.8 20.3 - - + +
240H ALA 2.9 9.5 + - - +
241H PHE* 3.5 30.2 - + + -
242H LYS* 2.8 28.4 + - - +
276H GLU* 2.8 30.9 + - + -
277H VAL* 1.3 85.2 - - - +
279H THR* 1.3 62.1 + - - +
314H TYR* 3.3 27.0 - + + +
316H PRO* 4.6 5.5 - - + +
322H LEU* 3.7 29.8 - - + +
325H ARG* 4.5 1.6 - - - -
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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