Contacts of the helix formed by residues 525 - 538 (chain P) in PDB entry 5G04
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 LEU 525 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519P TYR* 5.7 0.7 - - - +
520P TYR* 3.1 36.7 + - + +
523P CYS* 3.2 23.2 - - - +
524P LYS* 1.3 78.9 - - - +
526P TRP* 1.3 62.2 + - - +
527P ASP 3.7 1.6 - - - -
528P GLU* 3.6 29.9 + - + +
529P ALA* 3.3 15.6 + - - +
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Residues in contact with TRP 526 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521P PHE* 4.4 33.5 + + - -
524P LYS* 3.1 52.2 + - + -
525P LEU* 1.3 71.2 - - - +
527P ASP* 1.3 66.2 + - - +
529P ALA* 3.2 8.1 + - + +
530P SER* 2.9 29.1 + - - +
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Residues in contact with ASP 527 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525P LEU 3.7 0.2 - - - -
526P TRP* 1.3 76.7 - - - +
528P GLU* 1.3 65.2 + - + +
530P SER* 3.4 8.6 + - - -
531P THR* 3.3 24.3 + - - +
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Residues in contact with GLU 528 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520P TYR* 3.2 38.4 + - + -
525P LEU* 3.6 30.8 + - + +
526P TRP 3.3 0.6 - - - -
527P ASP* 1.3 78.7 - - + +
529P ALA* 1.3 61.4 + - - +
531P THR* 3.4 20.9 - - + +
532P CYS* 3.4 17.2 - - - -
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Residues in contact with ALA 529 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517P ALA* 3.5 25.9 - - + +
520P TYR* 3.6 16.0 - - + +
521P PHE* 4.0 11.2 - - + +
525P LEU 3.3 9.2 + - - +
526P TRP* 3.2 13.0 + - + +
528P GLU* 1.3 76.0 - - - +
530P SER* 1.3 59.3 + - - +
532P CYS* 3.3 6.4 + - - +
533P ALA* 2.8 31.5 + - - +
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Residues in contact with SER 530 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526P TRP* 2.9 19.1 + - - +
527P ASP* 3.4 9.5 + - - -
529P ALA* 1.3 75.5 - - - +
531P THR* 1.3 60.9 + - - +
533P ALA* 3.4 7.2 + - - +
534P GLN* 3.1 31.3 + - - +
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Residues in contact with THR 531 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527P ASP 3.3 11.9 + - - +
528P GLU* 3.4 22.7 - - + +
530P SER* 1.3 77.6 - - - +
532P CYS* 1.3 61.4 + - - +
534P GLN* 3.2 23.1 + - - +
535P LYS* 3.1 39.2 + - - +
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Residues in contact with CYS 532 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513P PHE* 4.4 16.4 - - + +
516P LEU* 3.8 28.0 - - - -
517P ALA* 4.0 18.2 - - + +
520P TYR* 4.2 11.4 - - - -
528P GLU 3.4 16.8 + - - +
529P ALA 3.3 9.5 + - - +
531P THR* 1.3 82.4 - - - +
533P ALA* 1.3 62.6 + - - +
535P LYS* 3.4 10.6 + - - +
536P CYS* 3.2 20.4 + - - +
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Residues in contact with ALA 533 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514P ARG* 6.2 0.2 - - - +
517P ALA* 3.9 13.2 - - + +
529P ALA 2.8 19.7 + - - +
530P SER* 3.7 8.3 - - - +
532P CYS* 1.3 72.7 - - - +
534P GLN* 1.3 61.3 + - - +
536P CYS* 3.3 10.4 + - - +
537P CYS* 3.3 25.8 + - - -
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Residues in contact with GLN 534 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530P SER* 3.1 20.7 + - - +
531P THR* 3.2 24.3 + - - +
533P ALA* 1.3 74.3 - - - +
535P LYS* 1.3 76.3 + - - +
537P CYS* 3.6 11.4 + - + +
538P ALA* 3.3 20.1 + - - +
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Residues in contact with LYS 535 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513P PHE* 4.6 21.6 - - + -
531P THR* 3.1 35.0 + - - +
532P CYS* 3.5 9.9 - - - +
533P ALA 3.3 0.4 - - - -
534P GLN* 1.3 90.0 - - - +
536P CYS* 1.3 61.3 + - - +
538P ALA* 3.1 26.5 + - + +
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Residues in contact with CYS 536 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511P THR 6.2 1.6 - - - -
513P PHE* 4.4 10.2 - - + +
514P ARG* 3.8 48.7 - - - +
532P CYS 3.2 9.6 + - - +
533P ALA* 3.4 14.1 - - - +
534P GLN 3.3 0.4 - - - -
535P LYS* 1.3 79.9 - - - +
537P CYS* 1.3 61.0 + - - +
538P ALA 3.5 3.6 + - - -
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Residues in contact with CYS 537 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533P ALA* 3.3 17.5 + - - -
534P GLN* 3.6 13.0 - - - +
536P CYS* 1.3 79.6 - - - +
538P ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 538 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534P GLN 3.3 9.9 + - - +
535P LYS* 3.1 23.3 + - + +
536P CYS 4.2 3.8 - - - -
537P CYS* 1.3 82.8 - - - +
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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