Contacts of the strand formed by residues 431 - 435 (chain M) in PDB entry 2JA7
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 LYS 431 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377M PRO* 4.8 14.8 - - + +
378M GLU 3.2 12.3 - - - +
379M VAL* 4.2 21.1 - - + -
405M VAL* 3.5 3.1 - - - +
406M ILE* 2.7 69.1 + - + +
429M GLY 4.0 6.3 + - - -
430M TRP* 1.3 73.8 - - - +
432M VAL* 1.3 64.1 + - - +
433M GLU 5.2 0.9 - - - +
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Residues in contact with VAL 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376M TYR 4.0 2.1 - - - +
378M GLU 2.7 17.2 + - - +
380M VAL* 3.3 31.9 - - + -
388M LEU* 3.2 25.7 - - + +
392M VAL* 3.5 28.5 - - + -
402M ALA* 4.3 11.9 - - + -
404M TYR 3.4 4.5 - - - +
405M VAL* 3.6 17.0 - - + +
426M LEU* 3.6 10.8 - - + -
431M LYS* 1.3 74.5 - - - +
433M GLU* 1.3 68.5 + - - +
434M ARG* 2.8 11.4 + - - +
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Residues in contact with GLU 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347M PHE* 3.9 11.6 - - - -
375M THR* 3.3 31.2 - - + +
376M TYR 3.6 9.2 - - - -
377M PRO* 3.9 23.0 - - + +
402M ALA* 3.1 14.9 - - - +
403M LYS* 3.2 11.2 + - + -
404M TYR* 2.8 44.8 + - + +
406M ILE* 4.4 15.5 - - + -
412M ARG* 3.7 1.5 + - - +
431M LYS 3.9 0.8 - - - -
432M VAL* 1.3 69.9 - - - +
434M ARG* 1.3 57.2 + - - +
1108N ARG* 2.6 33.9 + - - -
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Residues in contact with ARG 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375M THR* 2.6 23.6 + - - -
376M TYR* 2.8 59.1 + - + +
378M GLU* 2.9 41.7 + - + +
387M ARG* 4.8 1.6 - - - +
388M LEU* 5.2 1.1 - - + -
391M LEU* 3.7 25.1 - - + -
401M GLY 3.7 2.7 - - - +
402M ALA* 3.2 17.7 - - + -
403M LYS* 5.0 0.9 - - - -
432M VAL 2.8 10.1 + - - +
433M GLU* 1.3 73.7 - - - +
435M HIS* 1.3 75.5 + - - +
437M MET* 3.9 18.4 - - - +
440M ASP* 2.6 40.6 + - - -
498M ARG* 4.3 1.4 - - - +
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Residues in contact with HIS 435 (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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371M ALA 3.3 7.4 - - - +
372M LYS* 2.9 49.4 + - + -
374M LEU 3.8 4.1 + - - -
376M TYR 4.8 0.2 - - - -
396M PRO* 3.7 26.2 - - + +
398M GLU 3.9 4.4 + - - -
399M HIS* 3.0 28.2 + - + +
401M GLY* 2.8 43.7 + - - +
402M ALA* 3.3 4.2 + - - -
403M LYS* 4.6 11.9 - - + +
434M ARG* 1.3 96.6 + - - +
436M ILE* 1.3 69.8 + - - +
437M MET* 3.2 7.3 - - + +
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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