Contacts of the strand formed by residues 580 - 585 (chain H) 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 580 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568H LEU* 4.4 11.2 - - + -
579H GLN* 1.3 75.0 - - - +
581H ARG* 1.3 59.6 + - - +
582H PHE* 3.4 29.2 - - + -
595H PHE* 3.4 9.2 - - - -
596H GLY* 3.2 24.7 + - - +
598H PHE* 3.8 20.8 - - + -
609H ILE* 3.8 38.8 - - + -
611H PHE* 4.0 16.4 - - + -
629H VAL* 3.5 17.9 - - + -
630H GLN 3.5 3.8 - - - +
631H LEU* 3.7 20.4 - - + +
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Residues in contact with ARG 581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579H GLN 3.8 0.6 + - - +
580H ILE* 1.3 72.3 - - - +
582H PHE* 1.3 69.1 + - - +
583H TYR* 2.9 37.4 - - + +
591H VAL* 3.8 26.1 - - - +
593H GLU* 2.8 33.8 + - + +
594H GLY 3.5 2.9 - - - -
595H PHE* 3.7 13.2 - - + -
628H PHE 3.8 0.3 - - - +
629H VAL* 3.4 2.1 - - - -
630H GLN* 2.7 58.3 + - + +
632H ARG* 3.2 36.8 - - + +
639H THR* 5.6 0.2 - - - +
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Residues in contact with PHE 582 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580H ILE* 3.4 16.6 - - + -
581H ARG* 1.3 76.4 - - - +
583H TYR* 1.3 65.6 + - - +
592H TRP* 4.0 16.6 - - + -
593H GLU* 3.2 1.4 - - - -
594H GLY 2.5 41.8 + - - +
595H PHE 4.3 2.5 - - - -
596H GLY 4.3 1.3 - - - -
611H PHE* 3.4 39.9 - + - -
613H THR* 4.1 5.6 - - - -
614H PRO* 3.5 27.6 - - + -
627H VAL* 4.6 1.8 - - + -
628H PHE 3.1 8.7 - - - +
629H VAL* 4.0 16.8 - - + -
645H PHE* 3.9 37.2 - + - -
647H TYR* 4.1 16.6 - + - -
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Residues in contact with TYR 583 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581H ARG* 2.9 41.1 - - - +
582H PHE* 1.3 79.1 - - - +
584H GLU* 1.3 67.8 + - - +
585H GLU 5.1 1.3 - - - -
591H VAL* 3.8 15.3 - - + -
592H TRP* 2.8 20.9 - - - +
593H GLU* 4.0 3.8 - - - -
627H VAL* 3.1 5.6 - - - +
628H PHE* 2.7 70.6 + + + +
630H GLN* 3.6 22.6 + - + -
642H PRO* 3.2 31.9 - - + +
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Residues in contact with GLU 584 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583H TYR* 1.3 84.0 - - - +
585H GLU* 1.3 78.4 + - - +
586H GLU* 3.3 5.6 + - - +
591H VAL* 2.8 20.7 - - - +
592H TRP* 2.9 19.8 + - + +
616H TYR* 2.6 31.2 + - - -
617H LYS* 3.8 15.6 + - - +
625H ALA* 4.7 5.9 - - - +
626H SER 3.5 17.5 - - - +
627H VAL* 3.6 20.6 - - + +
628H PHE* 5.1 2.5 - - - -
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Residues in contact with GLU 585 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583H TYR* 4.6 4.2 - - - -
584H GLU* 1.3 84.5 - - - +
586H GLU* 1.3 88.8 + - - +
589H GLY* 3.4 19.4 - - - +
590H GLY 3.4 10.4 - - - +
591H VAL* 4.0 4.0 - - - +
628H PHE* 5.5 5.7 - - + -
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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