Contacts of the strand formed by residues 578 - 585 (chain B) 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 ILE 578 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LEU* 5.1 3.4 - - + -
573B VAL* 3.5 33.4 - - + -
574B GLN 3.3 20.9 - - - +
575B LYS* 3.7 12.7 - - - +
576B ASP 3.6 3.0 + - - -
577B ASP* 1.3 79.2 - - - +
579B GLN* 1.3 77.6 + - - +
598B PHE* 2.9 32.1 - - + -
603B VAL* 4.5 5.8 - - + -
609B ILE* 3.7 22.7 - - + -
631B LEU* 4.1 16.2 - - + -
632B ARG 3.7 12.3 - - - +
633B ARG* 5.2 1.1 - - + +
634B LYS* 4.2 8.5 + - - +
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Residues in contact with GLN 579 (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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578B ILE* 1.3 84.3 - - - +
580B ILE* 1.3 66.3 + - - +
581B ARG 3.9 1.0 + - - -
595B PHE* 3.8 21.9 - - + -
596B GLY 6.1 0.2 - - - +
598B PHE* 3.8 8.7 - - + -
631B LEU* 3.6 4.3 - - - -
632B ARG* 3.0 85.4 + - - +
633B ARG 4.1 3.2 + - - -
634B LYS* 3.8 31.9 - - + +
637B LEU* 4.5 0.8 - - - +
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Residues in contact with ILE 580 (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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568B LEU* 5.1 4.9 - - + -
578B ILE* 5.2 0.4 - - + -
579B GLN* 1.3 76.4 - - - +
581B ARG* 1.3 58.8 + - - +
582B PHE* 3.7 15.5 - - + -
595B PHE* 3.2 8.9 - - - -
596B GLY* 2.9 31.0 + - - +
598B PHE* 3.0 36.4 - - + -
609B ILE* 4.2 21.8 - - + -
611B PHE* 4.3 24.7 - - + -
629B VAL* 3.4 30.3 - - + -
630B GLN 3.5 5.4 - - - +
631B LEU* 4.4 12.8 - - + -
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Residues in contact with ARG 581 (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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579B GLN 3.9 1.2 + - - +
580B ILE* 1.3 74.1 - - - +
582B PHE* 1.3 68.4 + - - +
583B TYR* 3.5 25.9 - - + +
591B VAL* 3.5 29.5 - - - +
593B GLU* 2.8 34.0 + - + +
594B GLY 3.5 2.2 - - - -
595B PHE* 3.6 26.5 - - + -
628B PHE 3.9 0.2 - - - +
629B VAL* 3.2 3.4 - - - -
630B GLN* 3.0 64.0 + - + +
632B ARG* 4.2 25.8 - - + +
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Residues in contact with PHE 582 (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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553B MET* 5.8 0.9 - - + -
580B ILE* 3.7 15.3 - - + -
581B ARG* 1.3 75.2 - - - +
583B TYR* 1.3 67.7 + - - +
592B TRP* 3.9 19.5 - - + -
593B GLU* 3.6 0.9 - - - -
594B GLY 2.5 48.4 + - - +
596B GLY 4.2 4.3 - - - -
611B PHE* 3.8 24.9 - + - -
613B THR* 4.2 5.8 - - - -
614B PRO* 3.2 33.2 - - + -
627B VAL* 4.9 1.6 - - + -
628B PHE 3.0 8.3 - - - +
629B VAL* 3.2 32.3 - - + -
645B PHE* 3.7 35.7 - + - -
647B TYR* 4.6 6.1 - + + +
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Residues in contact with TYR 583 (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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581B ARG* 3.5 34.1 - - + +
582B PHE* 1.3 79.6 - - - +
584B GLU* 1.3 65.3 + - - +
585B GLU 4.8 1.6 - - - -
591B VAL* 3.8 16.6 - - + -
592B TRP* 3.1 19.3 - - - +
593B GLU* 4.7 0.2 - - - -
627B VAL* 3.9 1.5 - - - +
628B PHE* 2.7 71.4 + + + +
630B GLN* 3.7 30.6 + - + -
642B PRO* 3.0 34.1 - - + +
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Residues in contact with GLU 584 (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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583B TYR* 1.3 79.2 - - - +
585B GLU* 1.3 78.0 + - - +
586B GLU* 3.4 6.1 - - - +
591B VAL* 2.9 17.2 - - - +
592B TRP* 3.1 23.1 + - + +
616B TYR* 2.7 31.3 + - - -
617B LYS* 4.1 16.8 + - - +
625B ALA* 4.4 6.1 - - - +
626B SER 3.8 15.0 - - - +
627B VAL* 3.9 18.9 - - + +
628B PHE* 5.2 2.9 - - - -
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Residues in contact with GLU 585 (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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583B TYR* 4.8 3.6 - - - -
584B GLU* 1.3 86.4 - - - +
586B GLU* 1.3 82.7 + - - +
589B GLY* 3.2 29.9 - - - +
590B GLY 4.0 3.6 - - - -
591B VAL* 4.1 4.0 - - - +
628B PHE* 5.6 4.2 - - + -
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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