Contacts of the helix formed by residues 374 - 379 (chain D) in PDB entry 2VGB
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 LEU 374 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373D MET* 1.3 93.9 - - - +
375D GLU* 1.3 64.0 + - - +
376D SER 3.3 2.9 - - - -
377D MET* 2.9 37.5 + - + +
383D PRO* 4.2 9.4 - - + -
387D GLU* 3.7 25.8 - - + +
388D THR 4.4 0.9 - - - +
391D VAL* 3.7 18.4 - - + -
404D LEU* 4.1 6.1 - - + -
407D GLU* 3.0 22.4 + - + +
417D ALA* 3.5 25.4 - - - +
420D MET* 4.0 13.7 - - + -
421D GLN* 3.6 21.5 - - + +
424D ILE* 4.4 6.5 - - + -
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Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LYS* 5.5 5.0 + - - -
384B THR* 4.9 13.6 - - + +
372D GLN* 3.1 51.0 + - + +
374D LEU* 1.3 73.8 - - - +
376D SER* 1.3 58.1 + - - +
378D ILE* 2.8 57.4 + - - +
379D THR* 5.5 0.2 - - - -
387D GLU* 3.5 7.9 + - - +
405D SER* 6.0 0.3 - - - -
406D GLY* 4.9 4.2 + - - -
407D GLU* 3.6 11.9 + - - +
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Residues in contact with SER 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU 3.0 0.2 + - - -
375D GLU* 1.3 76.8 - - - +
377D MET* 1.3 56.6 + - - +
379D THR* 2.9 10.5 + - - -
380D LYS* 2.9 41.5 + - - +
382D ARG 3.5 8.7 + - - -
383D PRO* 3.6 0.3 - - - +
384D THR* 3.3 24.1 + - - +
387D GLU* 2.5 34.1 + - - -
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Residues in contact with MET 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 2.9 28.2 + - + +
376D SER* 1.3 73.4 + - - +
378D ILE* 1.3 61.6 - - - +
379D THR 2.7 6.7 + - - -
380D LYS 3.1 18.8 + - - +
381D PRO* 3.2 30.7 - - + +
382D ARG* 4.4 0.4 - - - -
383D PRO* 3.9 38.1 - - + -
407D GLU* 4.7 4.0 - - + +
413D PHE* 3.5 21.3 + - + +
416D GLU* 3.9 26.5 - - + +
417D ALA* 3.9 29.2 - - + +
420D MET* 4.3 7.2 - - + -
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Residues in contact with ILE 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU 4.1 1.0 + - - -
375D GLU* 2.8 54.8 + - - +
377D MET* 1.3 71.4 - - - +
379D THR* 1.3 65.8 + - - +
406D GLY* 3.4 37.5 - - - +
407D GLU* 3.6 8.6 - - + +
410D LYS* 5.2 10.8 - - + -
411D GLY* 3.3 17.1 - - - +
412D ASN* 3.0 25.6 + - - +
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Residues in contact with THR 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376D SER* 2.9 6.1 + - - +
377D MET 2.8 1.1 - - - -
378D ILE* 1.3 88.6 + - - +
380D LYS* 1.3 73.1 + - + +
381D PRO* 4.8 0.5 - - - +
412D ASN* 4.9 9.8 + - - +
413D PHE* 3.9 11.9 - - - -
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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