Contacts of the helix formed by residues 583 - 592 (chain D) in PDB entry 2GL7
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 ASP 583 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524D HIS* 3.5 31.0 + - - +
528D ARG* 3.3 16.5 + - - -
580D LEU 3.4 1.6 + - - +
581D ALA 3.1 8.0 - - - +
582D ARG* 1.3 79.7 - - - +
584D VAL* 1.3 67.9 + - - +
585D HIS* 3.0 24.4 + - - +
586D ASN* 3.2 27.9 + - - +
587D ARG* 3.3 17.1 + - - +
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Residues in contact with VAL 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D ARG 4.0 0.6 + - - -
583D ASP* 1.3 77.8 + - - +
585D HIS* 1.3 92.2 - - + +
587D ARG* 3.2 40.6 + - - +
588D ILE* 3.4 22.1 + - + +
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Residues in contact with HIS 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ARG* 3.7 29.7 - - - +
583D ASP* 3.0 13.2 + - - +
584D VAL* 1.3 96.4 - - + +
586D ASN* 1.3 61.1 + - - +
588D ILE* 3.7 19.2 + - + +
589D VAL* 3.4 25.3 + - - +
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Residues in contact with ASN 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D HIS* 4.2 10.1 + - - +
528D ARG* 2.9 38.1 + - - +
533D ILE* 4.2 13.0 - - + +
580D LEU* 2.8 51.3 + - - +
581D ALA* 4.5 0.2 - - - -
583D ASP* 3.2 20.6 + - - +
584D VAL 3.1 0.8 - - - -
585D HIS* 1.3 76.5 - - - +
587D ARG* 1.3 59.4 + - - +
589D VAL* 3.3 5.8 + - - +
590D ILE* 2.9 37.0 + - + +
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Residues in contact with ARG 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581D ALA* 3.1 32.5 + - + +
582D ARG 4.4 8.7 + - - -
583D ASP 3.3 4.9 + - - +
584D VAL* 3.2 40.8 + - - +
586D ASN* 1.3 74.6 - - - +
588D ILE* 1.3 65.6 + - + +
590D ILE* 3.9 7.2 - - - +
591D ARG* 3.1 26.7 + - - +
620D GLU* 3.3 35.5 + - - -
621D LEU* 3.7 23.6 - - + +
623D GLN* 3.7 18.3 - - - +
624D ASP* 5.9 5.4 - - - +
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Residues in contact with ILE 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584D VAL* 3.4 24.6 + - + +
585D HIS* 3.9 24.2 - - + +
586D ASN 3.3 0.4 - - - -
587D ARG* 1.3 79.7 - - + +
589D VAL* 1.3 63.1 + - + +
591D ARG* 4.0 3.7 - - - +
592D GLY* 3.2 19.2 + - - -
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Residues in contact with VAL 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528D ARG* 4.2 19.5 - - + -
533D ILE* 3.7 28.7 - - + -
534D PRO* 4.6 6.3 - - + -
585D HIS 3.4 15.0 + - - +
586D ASN* 3.3 9.5 + - - +
587D ARG 3.3 0.2 - - - -
588D ILE* 1.3 81.0 - - + +
590D ILE* 1.3 61.3 + - - +
592D GLY* 3.3 9.8 + - - -
593D LEU* 3.3 23.4 + - + +
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Residues in contact with ILE 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D ILE* 3.7 22.7 - - + -
537D VAL* 5.6 2.9 - - + +
577D LEU* 4.1 28.3 - - + +
580D LEU* 4.8 2.5 - - + -
581D ALA* 3.9 30.1 - - + +
586D ASN* 2.9 26.3 + - + +
587D ARG* 3.9 4.5 - - - +
589D VAL* 1.3 76.2 - - - +
591D ARG* 1.3 61.5 + - - +
593D LEU* 3.5 10.8 + - - +
595D THR* 3.0 41.6 - - + +
599D PHE* 4.3 8.7 - - + -
617D VAL* 5.2 1.8 - - + -
621D LEU* 4.0 19.7 - - + -
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Residues in contact with ARG 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587D ARG 3.1 18.2 + - - +
588D ILE* 4.0 4.0 - - - +
590D ILE* 1.3 77.4 - - - +
592D GLY* 1.3 57.6 + - - +
593D LEU 3.1 5.2 + - - -
594D ASN* 3.2 14.9 + - - -
595D THR* 4.1 8.1 + - - -
596D ILE* 4.7 20.6 - - + +
621D LEU* 5.2 6.7 - - + -
627D ALA* 5.4 7.2 - - + -
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Residues in contact with GLY 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588D ILE 3.2 12.3 + - - -
589D VAL 3.3 6.2 + - - -
590D ILE 3.3 0.8 - - - -
591D ARG* 1.3 77.2 - - - +
593D LEU* 1.3 60.1 + - - +
594D ASN 3.4 3.1 + - - -
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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