Contacts of the helix formed by residues 362 - 376 (chain B) in PDB entry 2GPV
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 GLU 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B TYR* 4.0 4.9 - - - -
360B LYS 3.5 12.9 - - - +
361B LEU* 1.3 75.6 - - - +
363B LYS* 1.3 67.3 + - - +
364B GLU* 3.1 11.0 - - - +
365B GLU* 2.7 32.1 + - - +
366B PHE* 2.8 12.5 + - - +
402B TYR* 2.5 31.6 + - - +
406B GLN* 4.6 2.1 - - - +
407B HIS* 2.7 37.9 + - - -
413B ARG* 4.2 0.6 + - - -
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Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.7 20.9 - - + -
245B GLU* 3.8 37.2 + - - +
315B TYR* 3.2 42.1 + - + +
362B GLU* 1.3 72.4 - - - +
364B GLU* 1.3 70.2 + - - +
366B PHE* 4.1 6.3 - - + -
367B VAL* 2.9 30.4 + - + +
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B TYR* 3.3 27.5 + - + -
238B VAL* 4.1 9.5 - - + +
242B LEU* 4.0 23.3 - - + +
362B GLU* 3.8 5.2 - - - +
363B LYS* 1.3 86.7 + - - +
365B GLU* 1.3 61.1 + - - +
367B VAL* 3.4 13.0 - - - +
368B THR* 2.9 24.9 + - - -
402B TYR* 3.3 47.3 + - + +
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.4 14.8 - - + -
362B GLU* 2.7 50.2 + - - +
364B GLU* 1.3 76.3 - - - +
366B PHE* 1.3 58.7 + - - +
368B THR* 4.4 3.0 - - - -
369B LEU* 3.0 35.0 + - + +
399B LEU* 4.8 7.3 - - + +
402B TYR* 3.7 12.8 - - + -
403B GLU* 3.0 25.8 - - - +
413B ARG* 2.9 33.8 + - - -
417B MET* 3.1 19.8 - - + +
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Residues in contact with PHE 366 (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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245B GLU* 3.9 18.2 - - - -
311B LEU* 3.4 36.6 - - + -
312B GLY* 4.1 11.7 - - - -
315B TYR* 3.6 51.4 - + + -
316B ARG* 6.3 0.7 - - + -
361B LEU* 4.4 10.5 - - + +
362B GLU 2.8 8.2 + - - +
363B LYS* 3.1 10.3 + - - +
365B GLU* 1.3 73.9 - - - +
367B VAL* 1.3 80.2 + - + +
369B LEU* 3.1 6.6 + - - +
370B LYS* 3.0 62.2 + - + +
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Residues in contact with VAL 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.6 2.5 - - + +
241B LEU* 3.7 38.5 - - + +
242B LEU* 4.2 15.3 - - + +
245B GLU* 3.6 26.0 - - + +
282B TRP* 4.3 6.1 - - - +
363B LYS* 2.9 31.5 + - + +
364B GLU* 3.4 17.3 - - - +
366B PHE* 1.3 82.3 - - + +
368B THR* 1.3 69.3 + - - +
370B LYS* 3.3 19.4 + - - +
371B ALA* 3.3 8.7 + - - +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.9 17.0 - - - +
241B LEU* 3.8 16.8 - - + +
364B GLU 2.9 18.5 + - - -
365B GLU 4.4 1.8 - - - -
366B PHE 3.3 0.6 - - - -
367B VAL* 1.3 81.4 - - - +
369B LEU* 1.3 57.8 + - - +
371B ALA* 3.0 7.3 + - + +
372B ILE* 3.0 30.5 + - + +
395B LEU* 4.0 23.3 - - + +
398B ALA* 4.6 7.9 - - + -
399B LEU* 4.2 27.8 - - + +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 3.8 14.4 - - + +
356B TYR* 4.3 22.0 - - + +
361B LEU* 4.4 3.8 - - + -
365B GLU 3.0 26.0 + - - +
366B PHE* 3.1 5.4 + - - +
368B THR* 1.3 75.1 - - - +
370B LYS* 1.3 59.3 + - - +
372B ILE* 3.8 16.5 - - + +
373B ALA* 2.9 29.8 + - - +
399B LEU* 4.7 7.6 - - + -
417B MET* 3.9 52.3 - - + +
418B LEU* 5.0 1.8 - - + +
420B THR* 5.2 0.2 - - - +
421B LEU* 4.5 22.2 - - + +
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Residues in contact with LYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLU* 3.2 28.4 + - - -
246B PRO* 4.6 5.9 - - - +
279B ILE* 6.0 1.4 - - - +
282B TRP* 3.7 34.2 - - + +
308B ILE* 3.8 35.3 - - + +
311B LEU* 3.6 22.9 - - + -
312B GLY* 5.1 0.7 - - - +
366B PHE* 3.0 46.9 + - + +
367B VAL* 3.6 11.0 - - - +
368B THR 3.3 0.2 - - - -
369B LEU* 1.3 73.0 - - - +
371B ALA* 1.3 65.4 + - - +
373B ALA* 3.4 4.8 + - - +
374B LEU* 3.1 22.9 + - - +
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Residues in contact with ALA 371 (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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241B LEU* 3.9 24.2 - - + -
282B TRP* 3.8 9.4 - - + -
286B ILE* 4.1 17.4 - - + +
367B VAL 3.3 2.9 + - - +
368B THR* 3.0 11.0 + - - +
370B LYS* 1.3 79.3 - - - +
372B ILE* 1.3 58.2 + - - +
374B LEU* 3.3 3.9 + - - +
375B ALA 3.0 23.2 + - - -
395B LEU* 3.3 28.7 - - + +
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Residues in contact with ILE 372 (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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368B THR* 3.0 21.7 + - + +
369B LEU* 3.8 9.2 - - + +
371B ALA* 1.3 73.8 - - - +
373B ALA* 1.3 61.3 + - - +
374B LEU 3.0 1.3 - - - -
375B ALA* 4.5 1.8 - - - -
376B ASN* 2.8 32.1 + - + +
392B GLN* 5.4 1.3 - - + +
395B LEU* 3.9 39.3 - - + +
396B HIS* 4.3 6.3 - - + +
399B LEU* 3.9 30.5 - - + -
418B LEU* 4.4 9.9 - - + -
421B LEU* 4.1 20.9 - - + -
419E MET* 4.1 23.6 - - + -
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 3.6 5.0 - - - +
307B GLU* 3.7 26.1 - - + +
308B ILE* 5.2 4.5 - - + -
311B LEU* 4.8 1.1 - - + -
369B LEU 2.9 18.3 + - - +
370B LYS* 3.7 8.1 - - - +
371B ALA 3.4 0.2 - - - -
372B ILE* 1.3 77.6 - - - +
374B LEU* 1.3 57.2 + - - +
376B ASN* 4.0 2.8 - - - +
377B SER* 3.3 26.5 + - - -
421B LEU* 4.1 19.3 - - + +
424B LEU* 4.3 11.0 - - + -
425B ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 374 (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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282B TRP* 4.2 6.3 - - + -
283B ALA* 3.7 30.5 - - + -
286B ILE* 3.8 16.8 - - + -
289B PHE* 4.1 13.5 - - + -
300B LEU* 3.4 45.7 - - + +
301B LEU* 3.8 15.0 - - + +
304B ALA* 3.6 12.8 - - + +
308B ILE* 4.3 6.3 - - + +
370B LYS 3.1 12.9 + - - +
371B ALA 3.5 7.4 - - - +
372B ILE 3.0 0.6 - - - -
373B ALA* 1.3 75.0 - - - +
375B ALA* 1.3 66.4 + - - +
376B ASN 3.4 0.2 + - - -
377B SER* 3.3 18.4 + - - -
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Residues in contact with ALA 375 (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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300B LEU* 4.4 11.4 - - - +
371B ALA 3.0 16.3 + - - +
372B ILE* 4.0 2.9 - - - +
374B LEU* 1.3 78.5 - - - +
376B ASN* 1.3 57.2 + - - +
377B SER 3.4 2.3 + - - -
378B ASP 5.1 0.5 + - - -
388B VAL* 3.5 16.9 - - - +
391B LEU* 3.7 31.2 - - + -
392B GLN* 3.2 31.0 + - + +
395B LEU* 3.7 8.5 - - + -
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Residues in contact with ASN 376 (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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372B ILE* 2.8 21.8 + - + +
373B ALA* 4.0 5.6 - - - +
375B ALA* 1.3 71.4 - - - +
377B SER* 1.3 55.3 + - - +
378B ASP* 3.0 11.9 + - - +
392B GLN* 3.5 21.8 + - + +
421B LEU* 4.4 8.1 - - - +
425B ARG* 3.0 20.7 + - - +
355E LYS* 4.1 9.5 + - - -
419E MET* 3.3 59.7 + - + +
422E PRO* 4.3 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