Contacts of the helix formed by residues 373 - 384 (chain A) in PDB entry 4GV1
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 GLY 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLU* 2.9 25.9 + - - -
371A THR 3.4 3.3 + - - -
372A LEU* 1.3 76.5 - - - +
374A PRO* 1.3 70.9 - - - +
375A GLU* 3.4 3.6 - - - -
376A ALA* 3.4 3.5 + - - +
377A LYS* 3.0 26.4 + - - +
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Residues in contact with PRO 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU 4.6 0.2 - - - +
373A GLY* 1.3 84.7 - - - +
375A GLU* 1.3 77.2 + - + +
377A LYS* 3.5 19.8 + - - +
378A SER* 3.0 28.6 + - - -
406A ARG* 4.5 4.4 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 5.3 3.1 - - - +
251A ARG* 5.5 2.7 - - - +
373A GLY* 4.4 1.4 - - - -
374A PRO* 1.3 95.1 - - + +
376A ALA* 1.3 58.2 + - - +
378A SER* 3.3 7.7 + - - -
379A LEU* 2.9 26.3 + - - +
405A HIS* 3.5 6.6 - - - -
406A ARG* 3.9 31.6 - - + +
407A PHE* 3.9 26.0 - - + +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLU* 3.8 12.7 + - - +
343A MET* 3.9 10.3 - - + -
372A LEU* 3.7 28.3 - - + -
373A GLY 3.4 5.9 + - - +
374A PRO 3.4 0.2 - - - -
375A GLU* 1.3 75.7 + - - +
377A LYS* 1.3 58.4 + - - +
379A LEU* 3.4 2.6 + - - +
380A LEU* 3.0 36.0 + - - +
407A PHE* 3.7 26.7 - - + -
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.9 26.7 - - + -
369A PRO 5.3 1.8 - - - +
370A ARG* 5.6 7.0 + - - +
372A LEU* 3.3 46.0 + - + +
373A GLY 3.0 15.8 + - - +
374A PRO* 3.6 20.5 - - - +
376A ALA* 1.3 76.5 - - - +
378A SER* 1.3 54.1 + - - +
381A SER* 2.7 39.9 + - - +
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A PRO 3.0 13.4 + - - -
375A GLU 3.5 5.6 - - - -
377A LYS* 1.3 74.1 - - - +
379A LEU* 1.3 65.7 + - - +
381A SER* 3.7 5.8 - - - -
382A GLY* 3.0 20.1 + - - -
405A HIS* 2.9 20.2 + - - -
406A ARG* 3.0 33.8 + - - -
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A MET* 3.6 37.9 - - + -
343A MET* 5.0 1.3 - - + -
375A GLU 2.9 17.1 + - - +
376A ALA 3.7 3.4 - - - +
378A SER* 1.3 75.9 - - - +
380A LEU* 1.3 63.5 + - + +
382A GLY* 3.2 3.1 + - - -
383A LEU* 2.9 45.1 + - + +
392A LEU* 3.6 24.6 - - + +
402A ILE* 4.3 3.8 - - + -
405A HIS* 3.4 25.2 - - + +
407A PHE* 3.7 21.3 - - + -
408A PHE* 4.1 19.1 - - + -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLY* 3.7 14.8 - - - +
339A MET* 3.7 15.5 - - + -
340A TYR* 3.6 38.6 - - + +
343A MET* 4.0 18.4 - - + -
344A CYS* 4.5 2.9 - - - -
368A PHE* 3.6 20.9 - - + -
372A LEU* 3.9 23.1 - - + -
376A ALA 3.0 20.7 + - - +
379A LEU* 1.3 76.3 - - + +
381A SER* 1.3 61.3 + - - +
383A LEU* 3.3 7.1 + - + +
384A LEU* 2.9 40.2 + - + +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ILE* 4.6 10.2 - - - +
368A PHE* 3.4 22.3 - - - -
377A LYS* 2.7 26.1 + - - +
378A SER* 3.7 6.3 - - - -
380A LEU* 1.3 77.4 - - - +
382A GLY* 1.3 60.2 + - - +
384A LEU* 3.5 2.0 + - - -
385A LYS* 3.3 34.6 + - - +
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Residues in contact with GLY 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A SER 3.0 14.8 + - - -
379A LEU 3.6 2.9 - - - -
381A SER* 1.3 74.4 - - - +
383A LEU* 1.3 64.8 + - - +
384A LEU 3.4 0.5 + - - -
385A LYS* 3.5 15.8 - - - +
391A ARG* 3.3 9.4 - - - +
392A LEU* 2.9 37.2 + - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A TRP* 3.6 18.2 - - + +
333A TRP* 3.6 11.1 - - - -
335A LEU* 4.0 17.9 - - + -
336A GLY* 3.7 27.6 - - - +
339A MET* 4.6 2.2 - - - -
379A LEU* 2.9 42.8 + - + +
380A LEU* 3.3 5.1 + - + +
382A GLY* 1.3 76.5 - - - +
384A LEU* 1.3 58.1 + - - +
385A LYS 3.4 0.7 - - - -
391A ARG* 3.2 25.9 + - - -
392A LEU* 3.8 16.4 - - + +
402A ILE* 3.7 34.5 - - + -
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A TRP* 3.3 62.3 - - + +
336A GLY* 3.9 17.9 - - - +
337A VAL* 3.8 13.2 - - + +
340A TYR* 4.1 14.4 - - + -
348A PRO* 4.4 7.4 - - + -
349A PHE* 5.6 1.2 - - + -
366A ILE* 3.9 39.0 - - + +
380A LEU* 2.9 22.8 + - + +
381A SER* 3.7 5.4 - - - +
382A GLY 3.2 0.4 - - - -
383A LEU* 1.3 76.0 - - - +
385A LYS* 1.3 64.3 + - - +
386A LYS* 3.4 7.4 + - - +
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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