Contacts of the helix formed by residues 564 - 578 (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 SER 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A ASP* 4.9 1.3 + - - -
471A SER* 5.0 0.5 + - - -
500A ARG* 3.2 18.5 + - - +
527A SER* 5.0 4.2 - - - -
529A GLN* 3.8 26.5 + - - -
531A LEU* 3.6 30.8 - - - +
562A THR 3.3 0.6 + - - -
563A GLY* 1.3 70.1 - - - -
565A GLU* 1.3 79.0 + - - +
566A VAL 3.3 0.4 - - - -
567A SER* 3.1 20.3 + - - -
568A LEU* 3.7 6.4 + - - +
617A VAL* 4.7 1.4 - - - +
646A PHE* 5.0 0.8 - - - -
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Residues in contact with GLU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ARG* 2.8 33.1 + - - -
561A ALA* 3.7 1.8 - - - -
562A THR 2.9 7.0 + - - +
564A SER* 1.3 97.6 + - - +
566A VAL* 1.3 59.1 + - - +
567A SER 3.4 0.2 - - - -
568A LEU* 3.5 17.0 - - + +
569A SER* 2.9 32.2 + - - -
615A VAL* 3.3 34.8 - - + +
616A GLU* 3.6 12.0 - - - -
617A VAL* 3.1 36.4 + - + +
646A PHE* 4.3 6.6 - - - -
651A PHE* 4.4 0.2 - - + -
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Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA* 3.6 15.9 - - + -
534A LEU* 3.4 24.7 - - + -
549A LEU* 3.4 19.1 - - + -
561A ALA* 3.7 17.3 - - + +
562A THR 3.6 15.9 - - - +
563A GLY 3.1 15.6 + - - +
565A GLU* 1.3 75.3 - - - +
567A SER* 1.3 66.7 + - - +
569A SER* 3.0 6.1 + - - -
570A VAL* 2.9 24.8 + - - +
585A VAL* 4.4 7.0 - - + -
586A VAL 5.1 0.2 - - - +
587A SER* 3.7 22.0 - - - +
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Residues in contact with SER 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA* 5.5 1.1 - - - +
531A LEU* 3.9 15.2 - - - +
532A PRO* 3.8 32.3 - - - +
534A LEU* 4.0 16.5 - - - +
563A GLY 4.4 1.0 + - - -
564A SER* 3.1 14.2 + - - -
566A VAL* 1.3 79.2 - - - +
568A LEU* 1.3 63.8 + - - +
570A VAL* 3.1 5.4 + - - +
571A GLU* 3.0 29.4 + - - +
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A SER 4.0 3.6 - - - +
565A GLU* 3.4 26.2 + - + +
566A VAL 3.1 0.2 - - - -
567A SER* 1.3 82.8 + - - +
569A SER* 1.3 56.9 + - - +
571A GLU* 3.3 7.3 + - + +
572A ALA* 2.9 26.2 + - - +
615A VAL* 4.4 1.8 - - + -
646A PHE* 6.3 0.7 - - + -
651A PHE* 3.9 37.0 - - + +
652A THR* 3.5 30.7 - - - -
653A PRO* 3.5 13.4 - - + +
656A VAL* 3.7 24.5 - - + -
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Residues in contact with SER 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A LEU* 3.8 24.3 - - - +
561A ALA* 3.6 14.1 - - - +
565A GLU 2.9 23.0 + - - -
566A VAL* 3.0 5.8 + - - -
568A LEU* 1.3 74.0 - - - +
570A VAL* 1.3 60.5 + - - +
572A ALA* 3.2 9.8 + - - +
573A ALA* 2.9 28.4 + - - +
585A VAL* 4.0 12.5 - - - +
615A VAL* 3.8 19.4 - - - +
656A VAL* 4.7 1.5 - - - +
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Residues in contact with VAL 570 (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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534A LEU* 4.3 11.2 - - + -
549A LEU* 3.8 27.1 - - + -
550A GLN* 3.6 25.0 - - - +
566A VAL 2.9 19.4 + - - +
567A SER* 3.1 8.7 + - - +
569A SER* 1.3 76.5 - - - +
571A GLU* 1.3 67.6 + - - +
573A ALA* 3.2 19.6 + - - +
574A LYS* 3.3 29.2 + - - +
585A VAL* 4.3 9.9 - - + -
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Residues in contact with GLU 571 (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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567A SER* 3.0 19.0 + - - +
568A LEU* 3.6 8.5 - - - +
570A VAL* 1.3 80.0 - - - +
572A ALA* 1.3 65.2 + - - +
574A LYS* 3.0 50.6 + - - +
575A THR* 3.2 13.9 + - - -
653A PRO* 3.6 24.4 - - + +
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Residues in contact with ALA 572 (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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559A LEU* 4.3 4.5 - - + -
568A LEU 2.9 17.2 + - - +
569A SER* 3.2 6.7 + - - +
571A GLU* 1.3 76.0 - - - +
573A ALA* 1.3 57.5 + - - +
575A THR* 3.1 6.0 + - - -
576A LEU* 2.9 33.5 + - + +
653A PRO* 3.5 27.1 - - - +
656A VAL* 3.5 27.1 - - + -
657A ALA* 3.9 4.6 - - - +
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Residues in contact with ALA 573 (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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550A GLN* 3.9 18.2 - - - +
559A LEU* 4.6 0.8 - - - +
569A SER 2.9 12.6 + - - +
570A VAL 3.3 11.0 - - - +
571A GLU 3.1 0.2 - - - -
572A ALA* 1.3 78.2 - - - +
574A LYS* 1.3 56.7 + - + +
576A LEU* 3.7 7.3 - - - +
577A ALA* 2.8 30.5 + - - +
581A ILE 4.7 0.9 - - - +
583A ALA* 4.3 24.8 + - + +
585A VAL* 4.3 7.4 - - + -
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Residues in contact with LYS 574 (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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550A GLN* 5.2 2.8 - - - +
570A VAL* 3.3 24.7 + - - +
571A GLU* 3.0 43.8 + - - +
573A ALA* 1.3 74.1 - - + +
575A THR* 1.3 67.7 + - - +
577A ALA* 3.3 7.8 + - - +
578A ALA* 3.0 22.2 + - - +
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Residues in contact with THR 575 (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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571A GLU 3.2 8.8 + - - -
572A ALA* 3.1 9.5 + - - -
574A LYS* 1.3 79.7 - - - +
576A LEU* 1.3 61.8 + - + +
578A ALA* 3.2 20.2 + - + +
579A LYS* 3.5 26.2 + - - +
653A PRO* 4.2 8.3 - - - +
654A GLU* 4.1 26.1 + - + -
657A ALA* 3.8 20.6 - - + -
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Residues in contact with LEU 576 (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* 4.6 4.9 - - + -
559A LEU* 4.3 9.9 - - + -
572A ALA 2.9 20.1 + - - +
573A ALA* 3.7 4.3 - - - +
575A THR* 1.3 75.4 - - + +
577A ALA* 1.3 59.4 + - - +
579A LYS* 2.9 21.8 + - + -
581A ILE* 2.9 45.9 + - + +
583A ALA* 3.8 24.9 - - + -
657A ALA* 3.6 32.5 - - + +
660A ALA* 3.8 22.9 - - + -
661A GLN* 4.1 18.6 - - + +
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Residues in contact with ALA 577 (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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573A ALA 2.8 17.4 + - - +
574A LYS* 3.3 8.5 + - - +
576A LEU* 1.3 76.0 - - - +
578A ALA* 1.3 58.8 + - - +
579A LYS 3.0 0.2 - - - -
580A ASN* 2.9 19.1 + - - -
581A ILE 3.3 13.2 + - - +
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Residues in contact with ALA 578 (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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574A LYS 3.0 13.1 + - - +
575A THR* 3.3 15.9 - - + +
576A LEU 3.1 0.2 - - - -
577A ALA* 1.3 75.8 - - - +
579A LYS* 1.3 59.6 + - + +
580A ASN 3.3 1.2 + - - -
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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