Contacts of the helix formed by residues 357 - 370 (chain B) in PDB entry 1GPU
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 ALA 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B VAL* 1.3 77.9 - - - +
358B THR* 1.3 62.9 + - - +
359B ARG* 3.0 8.1 - - + +
360B LYS* 2.9 21.1 + - + +
361B LEU* 3.0 10.6 + - - +
527B SER 3.7 4.5 - - - +
528B ARG* 3.3 32.1 - - - +
529B GLN 3.2 18.4 - - - +
530B ASN* 3.3 10.6 + - - +
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Residues in contact with THR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL 3.6 1.1 + - - +
357B ALA* 1.3 72.9 - - - +
359B ARG* 1.3 56.1 + - - +
361B LEU* 3.7 15.4 - - + +
362B SER* 2.9 29.5 + - - -
501B PRO 3.3 23.9 + - - +
502B ALA 4.0 15.9 - - - +
507B VAL* 3.9 15.3 - - + +
525B ALA 4.6 0.2 + - - -
526B LEU* 3.4 21.3 - - - +
527B SER* 2.7 38.3 + - - -
531B LEU* 4.1 10.3 - - + +
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA* 4.5 3.3 - - + +
358B THR* 1.3 78.3 + - - +
360B LYS* 1.3 59.7 + - - +
362B SER* 3.4 7.1 - - - -
363B GLU* 3.3 18.4 + - - +
385B PRO 4.7 3.2 + - - -
386B SER* 3.0 35.1 + - - +
387B ASN 4.0 8.6 - - - +
388B LEU* 3.6 27.5 - - + +
468B THR* 4.0 10.3 - - + -
469B HIS* 3.6 25.2 + - - -
526B LEU* 4.0 10.1 - - + -
527B SER 3.0 21.0 + - - +
528B ARG* 3.8 31.4 + - - +
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Residues in contact with LYS 360 (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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356B VAL* 3.5 19.5 - - + -
357B ALA* 2.9 15.5 + - + +
359B ARG* 1.3 79.0 - - - +
361B LEU* 1.3 63.2 + - - +
362B SER 3.1 0.4 - - - -
363B GLU* 2.8 35.2 + - - +
364B THR* 3.0 29.3 + - - +
388B LEU* 4.0 19.2 - - + +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TYR* 3.4 38.7 + - + +
356B VAL* 3.7 33.4 - - + +
357B ALA 3.0 10.6 + - - +
358B THR* 3.7 23.3 - - + +
359B ARG 3.4 0.2 - - - -
360B LYS* 1.3 76.4 - - - +
362B SER* 1.3 63.6 + - - +
364B THR* 3.2 7.9 + - - +
365B VAL* 3.0 25.6 + - - +
503B ASP* 3.7 7.9 - - - +
504B GLY* 3.4 32.1 - - - +
507B VAL* 3.9 14.1 - - + -
533B GLN* 4.6 3.8 - - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR 2.9 17.9 + - - -
359B ARG 3.4 7.0 - - - -
360B LYS 3.1 0.2 - - - -
361B LEU* 1.3 77.3 - - - +
363B GLU* 1.3 64.0 + - - +
365B VAL* 3.1 4.4 + - - +
366B LEU* 3.1 26.7 + - - +
387B ASN 5.3 1.4 + - - -
388B LEU 5.2 0.9 + - - -
466B VAL* 3.8 6.6 - - - +
507B VAL* 3.9 9.6 - - - +
511B TYR* 2.6 32.6 + - - -
526B LEU* 3.6 22.2 - - - +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ARG 3.3 3.3 + - - +
360B LYS* 2.8 44.0 + - - +
362B SER* 1.3 80.1 - - - +
364B THR* 1.3 56.5 + - - +
366B LEU* 3.4 6.8 + - - +
367B GLU* 3.0 36.2 + - + +
388B LEU* 3.3 54.7 + - + +
390B ARG 4.7 11.9 - - - +
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Residues in contact with THR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PRO* 4.0 4.7 - - + -
349B TYR* 4.0 20.2 + - - +
360B LYS* 3.0 21.4 + - - +
361B LEU* 3.5 10.1 - - - +
362B SER 3.2 0.2 - - - -
363B GLU* 1.3 75.6 + - - +
365B VAL* 1.3 64.4 + - - +
367B GLU* 3.3 6.6 + - + +
368B ASP* 2.9 48.7 + - - +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.9 21.3 - - + -
347B PRO* 4.0 14.6 - - + -
349B TYR* 6.5 0.4 - - + -
361B LEU* 3.0 19.5 + - + +
362B SER 3.1 6.9 + - - +
364B THR* 1.3 74.7 - - - +
366B LEU* 1.3 65.5 + - + +
368B ASP* 3.0 10.6 + - - -
369B VAL* 3.0 22.8 + - + +
504B GLY 5.9 0.2 - - - +
507B VAL* 3.9 17.9 - - + -
508B SER* 3.9 22.4 - - - +
511B TYR* 3.7 31.2 - - + -
515B LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 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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362B SER* 3.1 16.7 + - - +
363B GLU* 3.6 6.5 - - - +
365B VAL* 1.3 78.8 - - - +
367B GLU* 1.3 62.6 + - - +
369B VAL* 4.1 6.3 - - + -
370B TYR* 3.0 31.6 + - - +
376B LEU* 4.5 9.6 - - + -
388B LEU 4.1 5.6 - - - +
389B THR* 3.6 28.5 - - + +
391B TRP* 4.8 9.6 - - + +
438B TYR* 3.5 49.4 - - + +
511B TYR* 4.0 31.6 - - + +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 3.0 27.7 + - + +
364B THR* 3.6 8.3 - - + +
365B VAL 3.2 0.2 - - - -
366B LEU* 1.3 76.7 - - - +
368B ASP* 1.3 65.6 + - - +
370B TYR* 3.2 39.9 + - - -
371B ASN* 5.9 0.5 - - - +
391B TRP* 3.7 11.3 - - + +
392B LYS* 2.6 48.9 + - - +
393B GLU 5.2 0.3 + - - -
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Residues in contact with ASP 368 (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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345B LYS* 3.4 44.6 - - + +
347B PRO* 3.0 28.2 - - + +
364B THR* 2.9 24.9 + - - +
365B VAL 3.0 4.2 + - - +
367B GLU* 1.3 84.6 - - - +
369B VAL* 1.3 60.0 + - + +
371B ASN* 5.4 1.5 - - - +
372B GLN 5.4 0.2 + - - -
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 4.3 8.3 - - + -
345B LYS* 4.4 14.6 - - + +
346B LEU* 3.9 26.9 - - + -
365B VAL* 3.0 26.6 + - + +
366B LEU* 3.9 9.0 - - + +
368B ASP* 1.3 85.1 - - + +
370B TYR* 1.3 69.1 + - - +
371B ASN 3.2 3.1 - - - -
372B GLN* 3.0 10.1 + - + +
373B LEU* 2.9 39.5 + - + +
376B LEU* 4.2 13.7 - - + -
511B TYR* 6.3 0.2 - - + -
515B LEU* 4.9 7.0 - - + -
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Residues in contact with TYR 370 (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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366B LEU 3.0 17.2 + - - +
367B GLU* 3.2 41.8 + - - -
369B VAL* 1.3 78.1 - - - +
371B ASN* 1.3 83.6 + - + +
373B LEU 3.2 5.4 - - - +
376B LEU* 3.9 12.6 - - + -
391B TRP* 3.3 62.3 - + + -
393B GLU* 4.3 19.1 + - + +
410B ARG* 2.8 37.5 + - - +
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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