Contacts of the strand formed by residues 579 - 585 (chain D) in PDB entry 3GUT
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 GLN 579 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578D ILE* 1.3 81.1 - - - +
580D ILE* 1.3 65.3 + - - +
581D ARG 3.9 0.2 - - - -
595D PHE* 3.2 31.6 - - + -
598D PHE* 4.2 7.6 - - - -
631D LEU* 3.2 5.4 - - - -
632D ARG* 2.9 69.4 + - + +
634D LYS* 3.5 41.2 - - + +
637D LEU* 4.4 2.6 - - - +
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Residues in contact with ILE 580 (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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568D LEU* 4.6 4.3 - - + -
578D ILE* 5.0 0.2 - - + -
579D GLN* 1.3 78.4 - - - +
581D ARG* 1.3 58.7 + - - +
582D PHE* 3.3 29.4 - - + -
595D PHE* 3.4 9.7 - - - -
596D GLY* 3.0 30.0 + - - +
598D PHE* 3.7 23.0 - - + -
609D ILE* 3.8 33.2 - - + -
611D PHE* 4.2 20.2 - - + -
629D VAL* 3.6 17.7 - - + -
630D GLN 3.3 4.3 - - - +
631D LEU* 3.9 16.8 - - + -
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Residues in contact with ARG 581 (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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579D GLN 3.8 0.8 + - - -
580D ILE* 1.3 71.0 - - - +
582D PHE* 1.3 71.2 + - - +
583D TYR* 2.8 39.8 - - + +
591D VAL* 3.7 26.5 - - - +
593D GLU* 3.0 25.9 + - + +
594D GLY 3.7 2.5 - - - -
595D PHE* 3.8 17.9 - - + -
628D PHE 3.8 0.2 - - - +
629D VAL* 3.4 2.4 - - - -
630D GLN* 2.7 61.0 + - + +
632D ARG* 3.0 38.7 - - + +
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Residues in contact with PHE 582 (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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580D ILE* 3.3 28.5 - - + -
581D ARG* 1.3 77.7 - - - +
583D TYR* 1.3 67.1 + - - +
592D TRP* 3.9 16.8 - - + -
593D GLU* 3.7 1.6 - - - -
594D GLY 2.5 39.0 + - - +
595D PHE 4.3 0.9 - - - -
596D GLY 4.3 2.2 - - - -
611D PHE* 3.5 26.5 - + - -
613D THR* 4.3 4.9 - - - -
614D PRO* 3.6 31.2 - - + -
627D VAL* 4.6 1.6 - - + -
628D PHE 3.2 8.1 - - - +
629D VAL* 3.8 18.8 - - + +
645D PHE* 3.9 37.5 - + - -
647D TYR* 4.1 17.0 - + - -
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Residues in contact with TYR 583 (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 ARG* 2.8 51.1 - - - +
582D PHE* 1.3 76.6 - - - +
584D GLU* 1.3 66.6 + - - +
585D GLU 5.2 0.9 - - - -
591D VAL* 3.8 14.4 - - + -
592D TRP* 2.9 21.9 - - - +
593D GLU* 4.6 0.2 - - - -
627D VAL* 3.1 5.6 - - - +
628D PHE* 2.7 73.3 + + + -
630D GLN* 3.5 22.7 + - + -
642D PRO* 3.0 34.0 - - - +
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Residues in contact with GLU 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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583D TYR* 1.3 85.4 - - - +
585D GLU* 1.3 77.3 + - - +
586D GLU* 3.3 5.6 + - - +
591D VAL* 2.8 21.2 - - - +
592D TRP* 3.2 19.8 + - + -
616D TYR* 2.9 25.7 + - - -
617D LYS* 4.0 16.8 + - - +
625D ALA* 4.6 6.6 - - - +
626D SER 3.3 19.3 - - - +
627D VAL* 3.6 21.4 - - + +
628D PHE* 5.0 2.7 - - - +
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Residues in contact with GLU 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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583D TYR* 4.8 3.0 - - - -
584D GLU* 1.3 84.4 - - - +
586D GLU* 1.3 85.4 + - - +
589D GLY* 3.4 25.8 - - - +
590D GLY 4.1 2.7 - - - -
591D VAL* 4.0 3.6 - - - +
628D PHE* 5.6 5.1 - - + -
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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