Contacts of the strand formed by residues 541 - 544 (chain C) in PDB entry 2A2N
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 MET 541 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A PRO* 3.9 14.8 - - + -
535C ARG* 3.7 42.2 - - + +
537C ILE* 3.0 50.6 + - + +
540C PHE* 1.3 104.1 - - + +
542C ILE* 1.3 69.1 + - - +
543C GLN* 3.7 10.5 - - - +
593C PHE* 3.7 29.4 - - + -
594C ILE 3.3 15.0 - - - +
595C THR* 3.8 7.9 - - + +
596C VAL* 4.2 4.1 - - - +
623C SER* 5.3 0.2 - - - -
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Residues in contact with ILE 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ILE* 4.7 0.9 - - + -
533C PHE* 3.6 33.7 - - + -
535C ARG 3.9 4.0 - - - -
536C ILE* 4.0 8.5 - - + -
541C MET* 1.3 79.0 - - - +
543C GLN* 1.3 61.1 + - - +
544C THR* 5.5 0.2 - - - +
593C PHE* 3.1 3.8 - - - -
594C ILE* 2.9 51.7 + - + +
596C VAL* 5.1 2.0 - - + -
619C VAL* 3.9 23.6 - - + +
622C ILE* 3.7 27.1 - - + -
623C SER* 3.6 36.8 - - - +
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Residues in contact with GLN 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLU 3.0 24.2 + - - -
486A GLY* 3.5 8.4 - - - -
487A PRO* 3.6 3.4 - - - +
533C PHE* 3.1 23.1 - - - -
534C HIS* 3.1 23.1 + - - +
535C ARG* 2.9 53.3 + - + +
536C ILE* 4.8 0.2 - - - +
541C MET* 3.7 8.7 - - - +
542C ILE* 1.3 76.0 - - - +
544C THR* 1.3 66.4 + - - +
581C ALA* 3.8 6.3 - - + +
591C GLN* 2.9 25.2 + - - +
592C PHE 3.5 13.9 - - - +
593C PHE* 4.0 4.0 - - + -
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Residues in contact with THR 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531C HIS* 3.9 3.1 - - - +
532C THR 2.8 26.0 + - - -
533C PHE* 3.7 24.9 + - + -
534C HIS* 4.0 6.7 - - - -
542C ILE 5.5 0.4 - - - +
543C GLN* 1.3 77.2 - - - +
545C GLY* 1.3 66.4 + - - +
546C ASP 3.4 2.5 - - - -
591C GLN* 3.2 11.3 - - - +
592C PHE* 3.0 66.6 + - + +
640C ILE* 3.5 18.7 - - + +
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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
------------------------------------------------------------
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