Contacts of the strand formed by residues 608 - 612 (chain A) in PDB entry 6BM0
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 608 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A TRP* 3.1 25.8 - + + -
606A THR* 3.5 2.2 - - - -
607A VAL* 1.3 85.3 - - + +
609A ALA* 1.3 80.3 + - - +
610A GLY* 3.7 17.9 - - - -
619A VAL 5.0 1.3 - - - -
620A GLN* 3.7 1.3 - - - +
621A VAL* 3.1 25.9 + - + +
648A GLN* 6.1 0.4 - - - -
649A CYS* 2.8 39.0 - - - +
650A ALA* 5.0 0.2 - - - -
651A VAL* 2.8 55.9 - - + -
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Residues in contact with ALA 609 (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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536A TRP* 3.2 35.2 - - + +
537A THR 5.5 0.2 - - - +
538A VAL* 3.8 7.2 - - + +
576A ILE* 3.7 36.6 - - + -
600A PHE* 5.1 1.3 - - + -
606A THR* 5.6 1.1 - - - +
608A PHE* 1.3 80.4 - - - +
610A GLY* 1.3 59.5 + - - +
618A ILE* 5.5 0.4 - - + -
619A VAL 3.5 4.9 - - - +
620A GLN* 3.9 17.7 - - + +
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Residues in contact with GLY 610 (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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538A VAL* 4.0 10.4 - - - +
608A PHE* 3.7 19.8 - - - -
609A ALA* 1.3 75.4 - - - +
611A ASN* 1.3 66.4 + - - -
618A ILE* 4.9 0.2 - - - -
619A VAL* 2.8 34.3 + - - +
651A VAL* 4.8 2.8 - - - +
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Residues in contact with ASN 611 (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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537A THR 4.9 0.7 - - - +
538A VAL* 3.6 9.3 - - - +
539A ILE* 3.0 46.0 + - - +
610A GLY* 1.3 74.1 - - - -
612A ILE* 1.3 60.9 + - - +
615A ASN* 3.7 34.0 - - - +
617A TYR 3.6 6.6 + - - +
618A ILE* 3.4 20.0 - - - +
651A VAL* 3.9 15.4 - - - +
653A ASP 5.7 0.7 + - - -
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Residues in contact with ILE 612 (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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610A GLY 3.7 0.6 + - - -
611A ASN* 1.3 75.3 - - - +
613A GLY* 1.3 70.5 + - - +
614A ASP 3.5 1.6 + - - -
615A ASN 4.1 1.0 + - - -
616A ARG 3.9 3.1 + - - -
617A TYR* 2.7 51.4 + - + +
619A VAL* 3.7 22.0 - - + -
628A LEU* 5.9 2.0 - - + -
651A VAL* 3.3 31.0 - - + +
653A ASP 5.1 0.7 - - - +
654A PRO* 4.0 24.5 - - + -
655A TYR 4.1 2.7 - - - +
656A VAL* 3.8 13.2 - - + -
670A LEU* 3.8 33.7 - - + +
682A LEU* 5.8 2.9 - - + -
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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