Contacts of the helix formed by residues 652 - 668 (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 THR 652 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B LEU* 3.6 5.6 - - - -
647B LYS* 4.1 39.0 - - + +
650B GLY* 3.1 6.3 + - - -
651B PHE* 1.3 81.2 - - - +
653B PRO* 1.3 76.1 - - - +
654B GLU* 3.6 13.6 + - - +
655B GLY* 3.0 20.1 + - - -
656B VAL* 3.0 22.2 + - - +
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Residues in contact with PRO 653 (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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568B LEU* 3.7 15.3 - - + -
571B GLU* 3.6 42.4 - - + +
572B ALA* 3.5 14.9 - - + +
575B THR* 4.2 5.6 - - - +
652B THR* 1.3 87.1 - - - +
654B GLU* 1.3 73.1 + - - +
656B VAL* 3.4 0.6 + - + -
657B ALA* 3.0 29.1 + - - +
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Residues in contact with GLU 654 (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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575B THR* 4.1 17.8 + - + +
652B THR* 3.6 10.9 + - - +
653B PRO* 1.3 101.0 - - - +
655B GLY* 1.3 56.6 + - - +
657B ALA* 3.4 6.1 + - - +
658B GLU* 2.9 33.4 + - - +
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Residues in contact with GLY 655 (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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631B PHE* 4.4 0.9 - - - -
650B GLY* 3.6 12.8 - - - -
652B THR* 3.0 16.0 + - - -
654B GLU* 1.3 77.8 - - - +
656B VAL* 1.3 60.5 + - - +
658B GLU* 3.6 5.2 + - - +
659B ARG* 2.8 47.2 + - - +
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Residues in contact with VAL 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LEU* 4.4 10.1 - - + -
568B LEU* 3.7 29.4 - - + -
569B SER* 4.6 3.6 - - - +
572B ALA* 3.6 23.6 - - + -
613B MET* 3.5 20.3 - - + +
615B VAL* 3.9 17.3 - - + -
631B PHE* 4.0 24.5 - - + -
652B THR 3.0 14.1 + - - +
653B PRO 3.8 0.9 - - - +
655B GLY* 1.3 73.4 - - - +
657B ALA* 1.3 60.5 + - - +
659B ARG* 3.2 2.1 + - - -
660B ALA* 2.9 26.2 + - - +
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Residues in contact with ALA 657 (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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572B ALA* 3.9 6.0 - - - +
575B THR* 3.8 22.9 - - + -
576B LEU* 3.6 30.1 - - + +
579B LYS* 5.9 0.7 - - - +
653B PRO 3.0 18.4 + - - +
654B GLU 3.7 3.8 - - - +
656B VAL* 1.3 78.3 - - - +
658B GLU* 1.3 62.5 + - - +
660B ALA* 3.1 7.1 + - - +
661B GLN* 2.9 28.5 + - - +
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Residues in contact with GLU 658 (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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654B GLU 2.9 19.3 + - - +
655B GLY* 3.8 7.0 - - - +
656B VAL 3.3 0.2 - - - -
657B ALA* 1.3 76.0 - - - +
659B ARG* 1.3 66.6 + - + +
661B GLN* 3.0 17.5 + - + +
662B LYS* 3.0 50.6 + - + +
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Residues in contact with ARG 659 (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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680A PHE* 3.6 40.0 - - + +
613B MET* 3.7 9.4 - - + -
631B PHE* 3.2 49.9 - - - -
649B PHE 4.7 1.8 + - - -
650B GLY* 4.0 11.9 + - - -
655B GLY* 2.8 46.2 + - - +
656B VAL 3.2 5.4 + - - +
658B GLU* 1.3 86.2 - - + +
660B ALA* 1.3 57.3 + - - +
662B LYS* 3.3 7.7 + - + +
663B THR* 2.9 31.5 + - - -
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Residues in contact with ALA 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ILE* 3.7 24.8 - - + +
559B LEU* 4.2 10.1 - - + -
576B LEU* 3.9 25.1 - - + -
613B MET* 3.7 4.7 - - - -
656B VAL 2.9 13.8 + - - +
657B ALA* 3.1 9.6 + - - +
659B ARG* 1.3 77.5 - - - +
661B GLN* 1.3 57.1 + - - +
663B THR* 3.1 3.6 + - - -
664B ILE* 2.9 33.7 + - + +
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Residues in contact with GLN 661 (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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576B LEU* 4.0 5.2 - - + +
579B LYS* 3.3 42.7 + - - +
581B ILE* 3.7 25.5 - - + +
657B ALA* 2.9 18.1 + - - +
658B GLU* 3.4 16.6 - - + +
660B ALA* 1.3 77.5 - - - +
662B LYS* 1.3 63.9 + - + +
664B ILE* 3.3 10.1 + - - +
665B ALA* 3.0 24.3 + - - +
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Residues in contact with LYS 662 (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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679A ALA* 3.3 25.5 + - - +
680A PHE* 4.1 13.0 - - + +
658B GLU* 3.0 36.9 + - + +
659B ARG* 3.5 11.7 - - + +
660B ALA 3.2 0.2 - - - -
661B GLN* 1.3 76.4 - - + +
663B THR* 1.3 59.1 + - - +
665B ALA* 3.4 6.8 + - + +
666B PHE* 2.9 30.0 + - - +
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Residues in contact with THR 663 (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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679A ALA* 3.7 10.3 - - - +
680A PHE* 3.4 19.9 - - - -
557B ILE* 4.1 12.8 - - + -
611B PRO* 3.9 14.8 - - + -
612B ILE 5.2 1.8 - - - +
613B MET* 3.6 9.1 - - + -
629B GLN* 4.0 12.6 - - + +
659B ARG 2.9 17.3 + - - -
660B ALA 3.4 8.3 - - - -
662B LYS* 1.3 77.2 - - - +
664B ILE* 1.3 63.4 + - - +
666B PHE* 3.3 1.2 + - - +
667B TYR* 3.2 46.5 + - + -
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Residues in contact with ILE 664 (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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556B ASP* 3.8 30.1 - - + +
557B ILE* 4.0 18.4 - - + -
581B ILE* 3.7 35.0 - - + -
611B PRO* 4.6 7.2 - - + -
660B ALA* 2.9 23.0 + - + +
661B GLN* 3.6 11.2 - - - +
663B THR* 1.3 77.0 - - - +
665B ALA* 1.3 61.9 + - - +
667B TYR* 3.3 3.3 + - - +
668B LYS* 3.0 41.2 + - + +
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Residues in contact with ALA 665 (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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661B GLN 3.0 16.3 + - - +
662B LYS* 3.8 7.6 - - + +
664B ILE* 1.3 77.5 - - - +
666B PHE* 1.3 62.6 + - - +
667B TYR 3.3 0.5 + - - -
668B LYS* 3.3 24.4 + - - +
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Residues in contact with PHE 666 (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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673A ILE* 4.8 12.5 - - + +
677A LYS* 3.8 37.2 - - + -
678A LYS 3.6 13.0 - - - -
679A ALA* 3.5 22.9 - - + -
629B GLN* 3.7 9.9 - - - -
662B LYS 2.9 18.7 + - - +
663B THR 3.4 4.9 - - - +
665B ALA* 1.3 78.9 - - - +
667B TYR* 1.3 97.9 + + - +
668B LYS 5.0 0.9 - - - +
670B ASP* 3.6 9.4 - - - +
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Residues in contact with TYR 667 (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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673A ILE* 4.3 14.8 - - + -
611B PRO* 3.8 18.6 - - + -
628B HIS* 3.3 33.6 + + + +
629B GLN* 3.0 31.2 + - + -
663B THR* 3.2 25.9 + - + +
664B ILE 3.7 2.7 - - - +
666B PHE* 1.3 106.3 - + - +
668B LYS* 1.3 66.7 + - - +
669B GLY 3.1 0.5 + - - -
670B ASP* 2.9 34.0 + - - +
672B LEU* 3.6 36.3 - - + -
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Residues in contact with LYS 668 (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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664B ILE* 3.0 38.4 + - + +
665B ALA* 3.3 21.8 + - - +
666B PHE 5.0 0.9 - - - +
667B TYR* 1.3 77.5 - - - +
669B GLY* 1.3 59.8 + - - +
670B 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