Contacts of the strand formed by residues 578 - 582 (chain C) in PDB entry 2W4T
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 PHE 578 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C LEU* 3.8 15.7 - - + -
529C ILE* 6.3 2.0 - - + -
548C GLN* 5.9 1.1 - - + +
551C LEU* 5.0 12.6 - - + -
562C PHE* 3.3 41.3 - + + -
563C THR 3.8 2.0 - - - +
564C LYS* 5.5 0.2 - - - -
565C PRO* 3.8 14.7 - - - +
576C ALA* 3.7 0.9 - - - +
577C HIS* 1.3 80.5 + - + +
579C GLU* 1.3 65.6 + - - +
580C LEU* 3.9 16.2 - - + -
588C PRO* 3.2 4.6 - - - +
589C TYR* 2.7 79.1 + + + -
591C ILE* 3.2 31.2 - - + -
594C TRP* 6.4 0.4 - + - -
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Residues in contact with GLU 579 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C MET 2.7 19.8 - - - +
562C PHE* 3.8 1.2 - - - -
563C THR* 0.7 78.4 + - - +
564C LYS 4.5 4.0 - - - +
565C PRO* 4.7 4.7 - - + -
566C GLY 5.1 3.4 - - - +
578C PHE* 1.3 78.2 - - - +
580C LEU* 1.3 62.2 + - - +
581C HIS* 3.0 12.3 + - - -
586C ASN* 2.9 35.4 - - - +
587C VAL 3.2 11.0 - - - +
588C PRO* 4.4 5.8 - - + -
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Residues in contact with LEU 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C LEU* 4.0 25.4 - - + -
478C ASN* 5.7 2.0 - - - +
519C CYS* 5.8 4.7 - - + +
522C LEU* 4.3 18.6 - - + -
523C ILE* 5.5 7.9 - - + -
529C ILE* 5.1 15.3 - - + -
561C MET* 3.6 21.8 - - + +
562C PHE* 4.4 8.5 - - + -
578C PHE* 3.9 15.3 - - + -
579C GLU* 1.3 78.3 - - - +
581C HIS* 1.3 58.4 + - - +
582C HIS* 3.4 4.5 + - + +
586C ASN* 2.6 22.0 + - - -
587C VAL* 2.8 37.4 + - + +
589C TYR* 3.7 0.7 - - + +
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Residues in contact with HIS 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 5.0 1.7 - - - +
519C CYS* 4.4 4.2 - - - +
560C ARG* 3.8 11.4 + - - +
561C MET* 2.7 70.3 + - + +
563C THR* 3.0 13.6 - - + +
579C GLU* 3.0 21.4 + - - -
580C LEU* 1.3 71.5 - - - +
582C HIS* 1.3 64.5 + - - +
583C TYR 3.9 0.5 + - - -
585C GLY 4.0 2.2 - - - -
586C ASN* 3.0 30.2 + - - +
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Residues in contact with HIS 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C PHE* 3.3 7.9 - + + -
478C ASN* 2.0 56.2 + - - +
481C ASN* 4.1 0.4 - - + -
482C GLU* 2.3 23.7 + - + +
519C CYS* 5.5 0.7 - - - -
580C LEU* 3.4 4.0 + - + +
581C HIS* 1.3 76.9 - - - +
583C TYR* 1.2 177.5 + + - +
584C ALA* 2.7 17.0 - - - -
585C GLY 2.7 32.3 + - - +
587C VAL* 5.0 2.5 - - + -
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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
------------------------------------------------------------
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