Contacts of the helix formed by residues 652 - 668 (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 THR 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568A LEU* 3.5 6.3 - - - -
647A LYS* 4.1 37.5 - - + +
650A GLY* 3.1 5.5 + - - -
651A PHE* 1.3 81.2 - - - +
653A PRO* 1.3 78.1 - - - +
654A GLU* 3.5 12.8 + - - +
655A GLY* 2.9 28.4 + - - -
656A VAL* 3.0 14.2 + - - +
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Residues in contact with PRO 653 (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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568A LEU* 3.5 15.7 - - + -
571A GLU* 3.6 41.3 - - + +
572A ALA* 3.5 14.2 - - + +
575A THR* 4.2 5.2 - - - +
652A THR* 1.3 87.3 - - - +
654A GLU* 1.3 72.6 + - - +
656A VAL 3.4 0.5 + - - -
657A ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 654 (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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575A THR* 4.1 17.9 + - + +
652A THR* 3.6 10.5 + - - +
653A PRO* 1.3 98.8 - - - +
655A GLY* 1.3 58.5 + - - +
657A ALA* 3.7 6.4 - - - +
658A GLU* 2.9 33.8 + - - +
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Residues in contact with GLY 655 (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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631A PHE* 4.4 0.7 - - - -
650A GLY* 3.6 13.0 - - - -
652A THR* 2.9 16.0 + - - -
654A GLU* 1.3 77.8 - - - +
656A VAL* 1.3 60.1 + - - +
658A GLU* 3.9 5.4 - - - +
659A ARG* 2.9 47.3 + - - +
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Residues in contact with VAL 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LEU* 4.4 10.8 - - + -
568A LEU* 3.7 29.8 - - + -
569A SER* 4.7 2.9 - - - +
572A ALA* 3.5 25.1 - - + -
613A MET* 3.5 9.9 - - + +
615A VAL* 4.0 33.7 - - + -
631A PHE* 4.1 16.2 - - + -
652A THR 3.0 14.1 + - - +
653A PRO 3.7 0.9 - - - +
655A GLY* 1.3 73.2 - - - +
657A ALA* 1.3 60.2 + - - +
659A ARG* 3.3 2.1 + - - -
660A ALA* 2.9 26.0 + - - +
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Residues in contact with ALA 657 (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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572A ALA* 3.9 4.0 - - - +
575A THR* 3.8 28.5 - - + -
576A LEU* 3.6 30.9 - - + +
579A LYS* 5.9 0.9 - - - +
653A PRO 3.0 16.5 + - - +
654A GLU 3.7 4.3 - - - +
656A VAL* 1.3 78.1 - - - +
658A GLU* 1.3 56.8 + - - +
660A ALA* 3.0 7.2 + - - +
661A GLN* 2.9 27.9 + - - +
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Residues in contact with GLU 658 (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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654A GLU 2.9 19.1 + - - +
655A GLY* 3.9 7.6 - - - +
656A VAL 3.3 0.2 - - - -
657A ALA* 1.3 76.5 - - - +
659A ARG* 1.3 64.1 + - + +
661A GLN* 3.1 16.7 + - + +
662A LYS* 3.0 48.5 + - + +
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Residues in contact with ARG 659 (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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613A MET* 3.7 8.5 - - + -
631A PHE* 3.2 52.8 - - - -
649A PHE 4.7 2.0 + - - -
650A GLY* 3.9 11.3 + - - -
655A GLY* 2.9 34.8 + - - +
656A VAL 3.3 5.8 + - - +
658A GLU* 1.3 82.8 - - + +
660A ALA* 1.3 59.0 + - - +
662A LYS* 3.3 6.9 + - + +
663A THR* 2.9 32.4 + - - -
680B PHE* 3.7 39.3 - - + +
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Residues in contact with ALA 660 (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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557A ILE* 3.7 23.0 - - + +
559A LEU* 4.3 10.1 - - + -
576A LEU* 3.8 24.5 - - + -
613A MET* 3.8 4.9 - - + -
656A VAL 2.9 14.1 + - - +
657A ALA 3.2 10.1 - - - +
659A ARG* 1.3 77.8 - - - +
661A GLN* 1.3 55.9 + - - +
663A THR* 3.2 3.3 + - - -
664A ILE* 2.9 34.9 + - + +
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Residues in contact with GLN 661 (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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576A LEU* 4.1 5.7 - - + +
579A LYS* 3.5 40.9 + - - +
581A ILE* 3.8 24.1 - - + +
657A ALA* 2.9 14.5 + - - +
658A GLU* 3.1 20.1 + - + +
660A ALA* 1.3 78.7 - - - +
662A LYS* 1.3 63.0 + - + +
664A ILE* 3.3 9.3 + - - +
665A ALA* 3.0 24.8 + - - +
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Residues in contact with LYS 662 (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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658A GLU* 3.0 37.9 + - + +
659A ARG* 3.6 11.9 - - + +
661A GLN* 1.3 76.6 - - + +
663A THR* 1.3 58.1 + - - +
665A ALA* 3.5 5.8 + - + +
666A PHE* 2.9 29.5 + - - +
679B ALA* 3.3 25.6 + - - +
680B PHE* 4.2 13.4 - - + +
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Residues in contact with THR 663 (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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557A ILE* 4.1 13.7 - - + -
611A PRO* 4.0 14.1 - - + -
612A ILE 5.2 2.2 - - - +
613A MET* 3.6 8.9 - - + -
629A GLN* 4.0 12.9 - - + +
659A ARG 2.9 14.1 + - - -
660A ALA 3.2 8.3 + - - -
662A LYS* 1.3 74.7 - - - +
664A ILE* 1.3 65.5 + - - +
666A PHE* 3.2 1.0 + - - +
667A TYR* 3.1 47.3 + - + -
679B ALA* 3.7 9.9 - - - +
680B PHE* 3.4 20.1 - - - -
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Residues in contact with ILE 664 (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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556A ASP* 3.9 30.3 - - + +
557A ILE* 4.1 16.4 - - + -
581A ILE* 3.6 37.0 - - + -
611A PRO* 4.7 8.1 - - + -
660A ALA* 2.9 23.2 + - + +
661A GLN* 3.3 11.2 + - - +
663A THR* 1.3 75.6 - - - +
665A ALA* 1.3 63.8 + - - +
667A TYR* 3.2 3.5 + - - +
668A LYS* 3.0 42.0 + - + +
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Residues in contact with ALA 665 (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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661A GLN 3.0 16.1 + - - +
662A LYS* 3.9 7.4 - - + +
664A ILE* 1.3 78.6 - - + +
666A PHE* 1.3 63.7 + - - +
667A TYR 3.3 0.5 + - - -
668A LYS* 3.4 23.2 + - - +
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Residues in contact with PHE 666 (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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629A GLN* 3.7 7.4 - - - -
662A LYS 2.9 19.1 + - - +
663A THR 3.4 4.7 - - - +
664A ILE 3.2 0.2 - - - -
665A ALA* 1.3 78.5 - - - +
667A TYR* 1.3 100.9 + + - +
668A LYS 5.0 0.5 - - - +
670A ASP* 3.6 9.2 - - - +
673B ILE* 4.9 13.4 - - + +
677B LYS* 3.8 37.0 - - + -
678B LYS 3.6 13.7 - - - -
679B ALA* 3.5 22.7 - - + -
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Residues in contact with TYR 667 (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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611A PRO* 3.9 19.1 - - + -
628A HIS* 3.4 34.5 + + + +
629A GLN* 3.0 24.0 + - + -
663A THR* 3.1 36.1 + - + +
664A ILE 3.2 2.2 + - - +
666A PHE* 1.3 102.9 - + - +
668A LYS* 1.3 68.3 + - - +
669A GLY 3.1 0.5 + - - -
670A ASP* 2.8 34.2 + - - +
672A LEU* 3.6 35.6 - - + +
673B ILE* 4.3 14.1 - - + -
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Residues in contact with LYS 668 (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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664A ILE* 3.0 38.2 + - + +
665A ALA* 3.4 21.8 + - - +
666A PHE 5.0 0.5 - - - +
667A TYR* 1.3 77.4 - - - +
669A GLY* 1.3 61.9 + - - +
670A ASP* 3.4 4.9 + - - +
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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