Contacts of the helix formed by residues 377 - 383 (chain B) in PDB entry 2V4M
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 HIS 377 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B GLY 4.8 2.6 + - - -
374B LEU 2.9 4.1 + - - +
376B ASP* 1.3 97.0 + - + +
378B ILE* 1.3 60.1 + - - +
379B LYS* 3.2 3.8 - - - -
380B GLU* 3.1 22.8 + - - +
381B ILE* 3.0 35.9 + - + +
460B LEU* 5.1 8.7 - - + -
477B ASP* 3.6 38.5 + - + +
478B CYS* 3.5 29.4 - - + +
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Residues in contact with ILE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B LEU* 2.8 22.2 + - + +
375B LYS* 4.3 14.8 - - - +
376B ASP 3.8 0.4 - - - -
377B HIS* 1.3 75.9 - - - +
379B LYS* 1.3 64.0 + - + +
381B ILE* 4.0 9.6 - - + -
382B GLN* 2.9 46.4 + - - +
506B PHE* 4.4 14.1 - - + -
509B MET* 4.0 38.6 - - + -
510B MET* 4.2 22.2 - - - -
512B ASP* 6.1 0.2 - - - +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B LYS 5.8 2.2 - - - -
376B ASP* 4.5 16.3 + - - +
377B HIS 5.0 1.8 - - - -
378B ILE* 1.3 84.2 - - + +
380B GLU* 1.3 69.7 + - + +
382B GLN* 3.4 15.8 + - - +
383B ARG* 3.3 28.9 + - - +
456D GLU 5.8 1.6 + - - -
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ASP 5.9 0.2 - - - +
377B HIS* 3.1 22.2 + - - +
379B LYS* 1.3 83.8 - - + +
381B ILE* 1.3 65.3 + - - +
383B ARG* 3.1 28.2 + - - +
384B CYS* 3.3 13.0 + - - -
460B LEU* 3.8 16.1 - - + +
431D ARG* 3.2 36.5 + - + +
456D GLU 4.4 7.4 - - - +
457D ARG 3.6 25.3 - - - +
458D GLY* 3.9 4.0 + - - -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B LEU* 4.8 8.3 - - + -
377B HIS* 3.0 24.1 + - + +
378B ILE* 3.9 11.2 - - + +
380B GLU* 1.3 74.9 - - - +
382B GLN* 1.3 57.9 + - - +
384B CYS* 3.1 22.6 + - - +
387B LEU* 5.0 2.1 - - + +
412B LEU* 5.1 0.7 - - - +
434B VAL* 4.1 19.9 - - + +
460B LEU* 3.5 32.1 - - + -
462B VAL* 4.1 15.0 - - + -
478B CYS* 4.3 12.3 - - - -
506B PHE* 3.9 23.3 - - + -
510B MET* 3.9 26.3 - - + +
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ILE* 2.9 40.4 + - - +
379B LYS* 3.5 19.2 - - - +
380B GLU 3.2 0.6 - - - -
381B ILE* 1.3 76.0 - - - +
383B ARG* 1.3 60.9 + - + +
384B CYS 3.4 3.5 - - - +
412B LEU* 5.6 1.4 - - - +
509B MET 3.5 21.5 - - - +
510B MET* 3.6 39.2 - - + +
512B ASP* 3.9 10.2 - - - +
513B ASP* 6.0 0.3 - - - +
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B LYS* 3.3 16.2 + - - +
380B GLU* 3.1 21.7 + - - +
382B GLN* 1.3 77.3 - - + +
384B CYS* 1.3 65.6 + - - +
385B ARG* 4.4 8.5 + - - +
432B ASP* 5.6 1.0 - - - +
385C ARG* 5.1 2.1 + - - -
428D PRO* 5.8 0.6 - - - +
429D VAL 2.7 30.6 + - - +
430D PHE* 3.2 47.0 - - + +
431D ARG* 4.7 3.2 - - - +
457D ARG* 3.3 37.9 + - - +
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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