Contacts of the helix formed by residues 564 - 578 (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 SER 564 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B ASP* 4.9 0.9 + - - -
471B SER* 5.0 0.3 + - - -
500B ARG* 3.2 19.5 + - - +
527B SER* 4.9 5.3 - - - -
529B GLN* 3.8 26.5 + - - -
531B LEU* 3.7 31.2 - - - +
562B THR 3.3 0.6 + - - -
563B GLY* 1.3 69.9 - - - -
565B GLU* 1.3 77.4 + - - +
566B VAL 3.3 0.4 - - - -
567B SER* 3.1 21.0 + - - -
568B LEU* 3.8 6.2 + - - +
617B VAL* 4.6 1.4 - - - +
646B PHE* 4.9 0.8 - - - -
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Residues in contact with GLU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ARG* 2.9 32.9 + - - -
561B ALA* 3.7 2.7 - - - -
562B THR 2.9 6.8 + - - +
564B SER* 1.3 98.7 + - - +
566B VAL* 1.3 60.8 + - - +
568B LEU* 3.5 16.3 - - + +
569B SER* 2.9 32.7 + - - -
615B VAL* 3.3 34.9 - - + +
616B GLU* 3.7 12.5 - - - -
617B VAL* 3.1 36.7 + - + +
646B PHE* 4.2 6.6 - - - -
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Residues in contact with VAL 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 3.5 16.4 - - + -
534B LEU* 3.5 12.8 - - + -
549B LEU* 3.3 32.8 - - + -
561B ALA* 3.7 17.7 - - + +
562B THR* 3.7 15.0 - - - -
563B GLY 3.1 15.5 + - - +
565B GLU* 1.3 75.6 - - - +
567B SER* 1.3 67.2 + - - +
569B SER* 3.0 5.9 + - - -
570B VAL* 2.9 21.3 + - - +
585B VAL* 4.5 6.1 - - + -
586B VAL 5.4 0.2 - - - +
587B SER* 3.7 21.5 - - - +
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Residues in contact with SER 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA* 5.5 1.1 - - - +
531B LEU* 3.9 16.2 - - - +
532B PRO* 3.8 32.2 - - - +
534B LEU* 4.0 16.5 - - - +
563B GLY 4.4 1.0 + - - -
564B SER 3.1 14.1 + - - -
566B VAL* 1.3 78.4 - - - +
568B LEU* 1.3 63.7 + - - +
570B VAL* 3.1 7.3 + - - +
571B GLU* 3.0 29.5 + - - +
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B SER 4.0 3.8 - - - +
565B GLU* 3.5 27.5 - - + +
566B VAL 3.1 0.2 - - - -
567B SER* 1.3 82.9 + - - +
569B SER* 1.3 56.5 + - - +
571B GLU* 3.3 6.4 + - - +
572B ALA* 2.9 26.4 + - - +
615B VAL* 4.5 1.3 - - + -
646B PHE* 6.2 0.4 - - + -
651B PHE* 3.9 36.6 - - + +
652B THR* 3.6 6.3 - - - -
653B PRO* 3.6 35.8 - - + +
656B VAL* 3.7 24.9 - - + -
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Residues in contact with SER 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B LEU* 3.7 24.1 - - - +
561B ALA* 3.6 14.2 - - - +
565B GLU 2.9 22.6 + - - -
566B VAL* 3.0 6.7 + - - -
568B LEU* 1.3 74.5 - - - +
570B VAL* 1.3 60.6 + - - +
572B ALA* 3.5 9.1 - - - +
573B ALA* 2.9 28.4 + - - +
585B VAL* 4.0 12.0 - - - +
615B VAL* 3.7 19.6 - - - +
656B VAL* 4.6 1.7 - - - +
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU* 4.4 8.1 - - + -
549B LEU* 3.8 25.8 - - + -
550B GLN* 3.6 25.1 - - - +
566B VAL 2.9 18.9 + - - +
567B SER* 3.1 12.5 + - - +
569B SER* 1.3 75.8 - - - +
571B GLU* 1.3 68.9 + - - +
573B ALA* 3.2 16.1 + - - +
574B LYS* 3.3 33.5 + - - +
585B VAL* 4.4 10.1 - - + -
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Residues in contact with GLU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B PRO* 6.2 0.3 - - - +
567B SER* 3.0 19.1 + - - +
568B LEU* 3.6 6.3 - - + +
570B VAL* 1.3 78.7 - - - +
572B ALA* 1.3 64.1 + - - +
574B LYS* 3.0 48.8 + - - +
575B THR* 3.2 13.5 + - - -
653B PRO* 3.6 28.1 - - + +
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Residues in contact with ALA 572 (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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559B LEU* 4.3 4.5 - - + -
568B LEU 2.9 17.4 + - - +
569B SER 3.5 6.3 - - - +
571B GLU* 1.3 76.7 - - - +
573B ALA* 1.3 58.1 + - - +
575B THR* 3.1 5.5 + - - -
576B LEU* 2.9 33.0 + - - +
653B PRO* 3.5 27.3 - - - +
656B VAL* 3.6 26.9 - - + -
657B ALA* 3.9 5.1 - - - +
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Residues in contact with ALA 573 (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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550B GLN* 3.9 18.2 - - - +
559B LEU* 4.6 0.2 - - - +
569B SER 2.9 13.4 + - - +
570B VAL 3.3 11.2 - - - +
571B GLU 3.1 0.4 - - - -
572B ALA* 1.3 77.6 - - - +
574B LYS* 1.3 57.3 + - + +
576B LEU* 3.7 11.7 - - - +
577B ALA* 2.8 30.0 + - - +
581B ILE 4.7 0.9 - - - +
583B ALA* 4.2 22.0 + - + +
585B VAL* 4.2 7.0 - - + -
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Residues in contact with LYS 574 (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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550B GLN* 5.1 3.4 - - - +
570B VAL* 3.5 26.1 - - - +
571B GLU* 3.0 43.8 + - - +
573B ALA* 1.3 74.3 - - - +
575B THR* 1.3 67.8 + - - +
577B ALA* 3.2 8.0 + - - +
578B ALA* 3.1 22.2 + - - +
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Residues in contact with THR 575 (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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571B GLU 3.2 8.9 + - - -
572B ALA* 3.1 9.8 + - - -
574B LYS* 1.3 78.3 - - - +
576B LEU* 1.3 62.0 + - - +
578B ALA* 3.2 20.1 + - + +
579B LYS* 3.5 26.4 + - - +
653B PRO* 4.2 8.2 - - - +
654B GLU* 4.1 26.7 + - + -
657B ALA* 3.8 20.6 - - + -
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Residues in contact with LEU 576 (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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557B ILE* 4.6 4.7 - - + -
559B LEU* 4.4 6.5 - - + -
572B ALA 2.9 23.3 + - - +
573B ALA* 3.7 4.7 - - - +
574B LYS 3.2 0.2 - - - -
575B THR* 1.3 74.2 - - + +
577B ALA* 1.3 58.4 + - - +
579B LYS* 2.8 21.8 + - + +
581B ILE* 2.9 44.0 + - + +
583B ALA* 3.8 24.5 - - + -
657B ALA* 3.6 33.0 - - + +
660B ALA* 3.9 21.3 - - + -
661B GLN* 4.0 19.5 - - + +
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Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ALA 2.8 18.3 + - - +
574B LYS* 3.2 8.9 + - - +
576B LEU* 1.3 76.7 - - - +
578B ALA* 1.3 57.1 + - - +
580B ASN* 2.9 19.3 + - - +
581B ILE 3.4 12.9 + - - +
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Residues in contact with ALA 578 (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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574B LYS 3.1 12.2 + - - +
575B THR* 3.3 14.6 - - + +
576B LEU 3.1 0.2 - - - -
577B ALA* 1.3 75.8 - - - +
579B LYS* 1.3 57.8 + - + +
580B ASN 3.3 1.1 + - - -
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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