Contacts of the strand formed by residues 375 - 379 (chain M) in PDB entry 3HOU
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 THR 375 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347M PHE* 3.1 31.4 - - + -
373M THR 4.1 4.5 - - - +
374M LEU* 1.3 77.5 - - - +
376M TYR* 1.3 61.4 + - - +
403M LYS* 4.8 15.3 + - + +
404M TYR* 6.0 1.6 - - + -
433M GLU* 3.1 40.9 + - + +
434M ARG 2.8 20.3 + - - -
435M HIS* 5.0 0.7 - - - -
436M ILE* 3.8 10.1 - - - +
491M VAL* 4.2 3.1 - - - +
493M GLN* 3.3 18.2 - - - +
1107N ALA* 4.2 8.1 - - + +
1108N ARG* 5.1 1.1 - - - +
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Residues in contact with TYR 376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375M THR* 1.3 74.4 + - - +
377M PRO* 1.3 77.1 + - + +
378M GLU* 3.2 23.0 + - + -
433M GLU* 3.2 2.8 - - - -
434M ARG* 2.8 73.8 + - - +
436M ILE* 4.5 10.3 - - + -
440M ASP* 5.2 0.4 - - - +
491M VAL* 5.1 2.0 - - + -
492M PRO 3.5 19.5 - - - -
493M GLN 3.4 25.1 + - - -
494M SER 3.7 14.6 + - - -
495M GLU* 3.4 22.5 + - - +
498M ARG* 3.7 34.2 + - - +
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Residues in contact with PRO 377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376M TYR* 1.3 98.7 - - + +
378M GLU* 1.3 63.0 + - - +
379M VAL* 4.0 4.7 + - - +
406M ILE* 5.7 0.4 - - + -
431M LYS* 3.8 30.9 + - + +
432M VAL 4.2 3.4 - - - +
433M GLU* 4.2 22.0 - - + +
493M GLN* 3.3 46.6 - - + +
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Residues in contact with GLU 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376M TYR* 3.2 20.7 + - + -
377M PRO* 1.3 74.3 - - - +
379M VAL* 1.3 64.6 + - - +
384M ASN* 4.0 16.0 + - - +
387M ARG* 2.9 44.4 + - - -
388M LEU* 3.5 12.9 - - + +
431M LYS* 3.2 4.4 - - - +
432M VAL* 2.8 37.9 + - - +
434M ARG* 3.0 29.3 + - - +
117R PRO* 5.7 4.7 - - - +
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Residues in contact with VAL 379 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377M PRO 4.6 4.0 - - - +
378M GLU* 1.3 77.4 - - - +
380M VAL* 1.3 74.1 - - - +
381M THR* 3.2 7.0 + - - +
384M ASN* 3.2 17.5 + - - +
388M LEU* 4.2 1.6 - - - -
429M GLY* 4.0 14.1 - - - +
430M TRP 3.5 12.1 - - - +
431M LYS* 3.9 20.0 - - + -
102R SER* 3.7 35.7 - - - +
103R MET* 5.2 9.9 - - - -
104R ASN* 4.7 2.0 - - - +
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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