Contacts of the strand formed by residues 702 - 707 (chain A) in PDB entry 5BPW
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 THR 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597A LYS* 3.4 29.0 + - + -
617A ALA* 3.8 5.0 - - + +
618A ILE 3.9 8.7 - - - +
619A LYS* 3.4 43.1 - - + +
683A TYR* 3.0 20.6 - - - -
700A ILE 3.4 5.3 + - - -
701A PRO* 1.3 75.1 - - - +
703A ARG* 1.3 64.0 + - - +
704A THR* 3.8 4.3 + - - +
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Residues in contact with ARG 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A ILE* 4.0 20.2 - - + +
617A ALA 3.3 8.9 + - - +
618A ILE* 3.8 7.4 - - + +
619A LYS 3.2 22.4 + - - +
673A LEU 3.2 16.3 + - - -
674A VAL* 2.2 41.8 + - - +
676A ASN* 3.4 18.2 - - - +
679A ASP* 2.4 36.0 + - - -
680A SER* 3.7 17.4 - - - +
683A TYR* 3.6 35.3 - - + +
701A PRO 4.2 0.4 + - - -
702A THR* 1.3 73.8 - - - +
704A THR* 1.3 65.9 + - - +
705A MET* 3.5 21.3 + - + +
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Residues in contact with THR 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A LYS* 2.9 51.1 + - + +
621A GLY* 4.2 7.6 - - - -
683A TYR* 4.8 5.2 + - - -
702A THR 3.8 4.5 + - - -
703A ARG* 1.3 74.1 - - - +
705A MET* 1.3 65.6 + - - +
706A HIS* 3.9 33.3 + - + +
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Residues in contact with MET 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A ILE* 3.5 33.7 - - + -
619A LYS 3.0 8.4 + - - +
621A GLY 2.9 20.7 + - - -
669A LEU* 3.4 30.1 - - + -
670A PRO* 5.2 1.3 - - - +
673A LEU* 4.2 20.9 - - - +
674A VAL* 3.7 20.0 - - - -
703A ARG* 3.9 20.0 - - + +
704A THR* 1.3 80.8 - - - +
706A HIS* 1.3 61.9 + - - +
707A PHE* 3.5 25.8 - - + -
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Residues in contact with HIS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A GLY* 4.3 5.6 - - - -
622A SER* 3.5 31.8 + - - +
633A ARG* 4.0 16.5 + - - -
704A THR* 3.9 33.5 + - + +
705A MET* 1.3 75.3 - - - +
707A PHE* 1.3 61.9 + - - +
708A GLU* 3.7 4.9 + - - +
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Residues in contact with PHE 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A PHE* 3.2 39.5 - + + -
622A SER* 2.7 18.8 + - - +
623A PHE* 3.8 27.4 - + + -
624A THR* 3.0 26.6 + - - +
667A VAL* 3.7 12.6 - - + -
668A GLN 3.5 22.9 - - - -
669A LEU* 4.2 4.3 - - + -
670A PRO* 4.3 14.6 - - + -
705A MET* 3.5 40.8 - - + -
706A HIS* 1.3 72.2 - - - +
708A GLU* 1.3 60.7 + - - +
709A LYS 4.4 9.0 - - - +
711A TRP* 4.0 7.6 + - + -
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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