Contacts of the helix formed by residues 357 - 370 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A VAL* 1.3 78.9 - - - +
358A THR* 1.3 63.0 + - - +
359A ARG* 3.0 7.9 - - + +
360A LYS* 2.9 21.2 + - + +
361A LEU* 3.0 9.9 + - - +
527A SER 3.7 5.4 - - - +
528A ARG* 3.3 32.5 - - - +
529A GLN 3.2 17.7 - - - +
530A ASN* 3.4 10.2 + - - +
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Residues in contact with THR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL 3.6 1.5 + - - +
357A ALA* 1.3 72.3 - - - +
359A ARG* 1.3 56.1 + - - +
360A LYS 3.3 0.2 - - - -
361A LEU* 3.7 14.3 - - + +
362A SER* 3.0 28.2 + - - -
501A PRO 3.4 25.4 + - - +
502A ALA 4.0 15.5 - - - +
503A ASP* 4.4 0.2 - - - -
507A VAL* 3.9 14.7 - - + +
526A LEU* 3.4 22.1 - - - +
527A SER* 2.7 37.4 + - - -
531A LEU* 4.1 11.0 - - + +
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ALA* 3.0 4.7 - - + +
358A THR* 1.3 79.2 + - - +
360A LYS* 1.3 59.1 + - - +
362A SER* 3.4 4.7 - - - -
363A GLU* 3.3 18.9 + - - +
385A PRO 4.7 3.4 + - - -
386A SER* 2.9 36.3 + - - +
387A ASN 3.9 4.1 - - - +
388A LEU* 3.7 25.2 - - + +
468A THR* 3.9 17.7 - - + -
469A HIS* 3.6 23.9 + - - -
526A LEU* 4.0 11.0 - - + -
527A SER 3.0 22.6 + - - +
528A ARG* 4.0 26.1 + - - +
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Residues in contact with LYS 360 (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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356A VAL* 3.5 20.2 - - + -
357A ALA* 2.9 15.7 + - + +
359A ARG* 1.3 78.6 - - - +
361A LEU* 1.3 65.0 + - - +
362A SER 3.1 0.2 - - - -
363A GLU* 2.7 33.9 + - - +
364A THR* 3.0 29.4 + - - +
388A LEU* 4.0 19.0 - - + +
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Residues in contact with LEU 361 (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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349A TYR* 3.4 38.3 + - + +
356A VAL* 3.8 32.1 - - + +
357A ALA 3.0 12.1 + - - +
358A THR* 3.7 23.8 - - + +
360A LYS* 1.3 75.8 - - - +
362A SER* 1.3 62.8 + - - +
364A THR* 3.2 9.5 + - - +
365A VAL* 3.0 24.9 + - - +
503A ASP* 3.6 7.6 - - - -
504A GLY* 3.3 31.6 - - - +
507A VAL* 3.9 14.6 - - + -
533A GLN* 4.5 3.4 - - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR 3.0 18.3 + - - -
359A ARG 3.4 7.4 - - - -
361A LEU* 1.3 77.2 - - - +
363A GLU* 1.3 61.5 + - - +
365A VAL* 3.1 5.1 + - - +
366A LEU* 3.1 27.1 + - - +
387A ASN 5.3 1.1 + - - -
388A LEU 5.2 0.7 + - - -
466A VAL* 3.8 7.0 - - - +
507A VAL* 4.0 9.8 - - - +
511A TYR* 2.6 33.3 + - - -
526A LEU* 3.5 22.8 - - - +
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG 3.3 3.3 + - - +
360A LYS* 2.7 44.5 + - - +
362A SER* 1.3 78.8 - - - +
364A THR* 1.3 57.6 + - - +
366A LEU* 3.4 6.7 + - - +
367A GLU* 3.0 35.9 + - + +
388A LEU* 3.3 53.4 + - + +
390A ARG 4.6 12.5 - - - +
391A TRP* 6.1 0.2 - - - -
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 4.0 11.2 - - + -
349A TYR* 4.0 12.4 + - - +
360A LYS* 3.0 21.7 + - - +
361A LEU* 3.4 12.1 - - - +
362A SER 3.2 0.2 - - - -
363A GLU* 1.3 75.4 + - - +
365A VAL* 1.3 59.6 + - - +
367A GLU* 3.3 6.3 + - + +
368A ASP* 2.9 46.0 + - - +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.9 21.1 - - + -
347A PRO* 3.8 25.6 - - + -
349A TYR* 6.5 0.2 - - + -
361A LEU* 3.0 18.9 + - + +
362A SER 3.1 7.2 + - - +
364A THR* 1.3 75.0 - - - +
366A LEU* 1.3 65.0 + - - +
368A ASP* 3.1 2.1 + - - -
369A VAL* 3.0 34.5 + - + +
504A GLY 5.8 0.2 - - - +
507A VAL* 4.0 17.5 - - + -
508A SER* 4.0 12.6 - - - +
511A TYR* 3.7 31.2 - - + -
515A LEU* 5.9 0.4 - - + -
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 3.1 18.9 + - - +
363A GLU* 3.6 5.6 - - + +
365A VAL* 1.3 75.5 - - - +
367A GLU* 1.3 63.0 + - + +
369A VAL* 3.9 5.8 - - + +
370A TYR* 3.0 31.4 + - - +
376A LEU* 4.6 8.3 - - + -
388A LEU 4.1 6.7 - - - +
389A THR* 3.8 27.6 - - + +
390A ARG 6.2 0.2 - - - -
391A TRP* 4.8 9.2 - - + +
438A TYR* 3.6 48.5 - - + +
511A TYR* 3.9 33.0 - - + +
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Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLU* 3.0 27.5 + - + +
364A THR* 3.5 9.4 - - + +
366A LEU* 1.3 76.7 - - - +
368A ASP* 1.3 65.4 + - - +
370A TYR* 3.1 40.3 + - - -
371A ASN* 5.8 0.2 - - - +
391A TRP* 3.8 10.9 - - + +
392A LYS* 2.8 47.3 + - - +
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Residues in contact with ASP 368 (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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345A LYS* 3.3 45.6 - - - +
347A PRO* 3.1 25.5 - - + +
364A THR* 2.9 25.2 + - - +
365A VAL 3.1 4.7 + - - +
367A GLU* 1.3 84.4 - - - +
369A VAL* 1.3 60.5 + - + +
371A ASN* 5.4 1.1 - - - -
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 4.3 9.4 - - + -
345A LYS* 4.3 15.9 - - + +
346A LEU* 3.9 26.2 - - + -
365A VAL* 3.0 28.3 + - + +
366A LEU* 3.9 9.0 - - + +
368A ASP* 1.3 85.7 - - + +
370A TYR* 1.3 61.8 - - - +
371A ASN 3.2 3.1 - - - -
372A GLN* 3.1 9.7 + - + +
373A LEU* 2.9 49.5 + - + +
376A LEU* 4.4 9.0 - - + -
515A LEU* 4.9 7.4 - - + -
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Residues in contact with TYR 370 (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 LEU 3.0 17.7 + - - +
367A GLU* 3.1 43.9 + - - -
369A VAL* 1.3 77.2 - - - +
371A ASN* 1.3 82.7 + - + +
373A LEU 3.2 5.4 - - - +
376A LEU* 3.9 12.3 - - + -
391A TRP* 3.3 60.8 - + + -
393A GLU* 4.7 17.5 + - - +
410A ARG* 2.8 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