Contacts of the strand formed by residues 608 - 612 (chain E) in PDB entry 6Q2J
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 608 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523E LYS* 4.4 22.6 + - - +
543E TRP* 4.6 9.2 - - + -
556E SER* 3.3 26.0 - - - +
557E THR* 6.0 0.2 - - - -
607E GLY* 1.3 70.0 - - - -
609E CYS* 1.3 60.6 + - - +
610E ASN* 3.9 5.4 + - - +
619E PHE 3.4 2.3 - - - +
620E CYS* 3.3 1.7 - - - -
621E GLU 2.6 42.9 + - - +
622E PRO* 4.4 10.6 - - + +
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Residues in contact with CYS 609 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555E PHE* 3.8 19.1 - - + -
556E SER 3.4 8.1 + - - -
557E THR* 3.6 8.3 + - - -
583E GLN* 3.3 20.8 - - - +
602E ILE* 4.0 13.0 - - + -
605E GLY* 3.8 19.5 - - - -
607E GLY 3.5 7.6 + - - -
608E THR* 1.3 73.4 - - - +
610E ASN* 1.3 61.6 + - - +
611E CYS* 4.6 1.5 - - - -
619E PHE 3.1 4.7 - - - -
620E CYS* 2.0 48.5 - - - -
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Residues in contact with ASN 610 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E ALA* 3.6 9.2 - - - +
521E VAL 4.2 6.0 + - - +
522E SER 3.4 23.3 - - - +
523E LYS* 3.3 32.8 - - - +
557E THR* 5.5 0.2 - - - -
583E GLN* 5.3 0.7 - - - -
608E THR* 3.9 5.4 + - - +
609E CYS* 1.3 74.4 - - - +
611E CYS* 1.3 64.0 + - - +
612E PHE* 4.3 16.5 - - - -
618E CYS* 3.3 3.3 - - - -
619E PHE* 2.9 55.5 + - - +
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Residues in contact with CYS 611 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520E ALA* 3.0 26.3 + - + +
521E VAL* 3.9 6.1 - - - -
582E PRO* 3.9 22.7 - - + -
583E GLN* 4.0 25.4 - - - -
586E LEU* 5.4 0.7 - - + -
602E ILE* 4.1 5.8 - - - -
609E CYS 4.6 1.1 - - - -
610E ASN* 1.3 76.1 - - - +
612E PHE* 1.3 65.6 + - - +
613E PRO* 3.5 9.1 - - + +
617E LYS 3.5 4.0 - - - -
618E CYS* 2.0 47.6 - - - -
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Residues in contact with PHE 612 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B HIS* 5.7 11.9 - + + -
247B GLN 5.8 1.3 - - - -
249B ARG* 5.7 6.5 - - + -
521E VAL* 3.6 33.2 - - + -
523E LYS* 6.2 1.6 - - + -
586E LEU* 5.7 0.3 - - - +
610E ASN* 4.3 16.6 - - - -
611E CYS* 1.3 75.5 - - - +
613E PRO* 1.3 63.8 - - + +
614E GLU* 3.4 13.5 - - + +
615E GLU* 4.8 17.5 - - + +
616E GLU* 2.8 21.8 + - - -
617E LYS* 2.9 22.8 + - + +
619E PHE* 3.7 38.6 - + - -
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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