Contacts of the strand formed by residues 608 - 612 (chain K) in PDB entry 6R1U
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 VAL 608 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386K ILE* 5.7 0.4 - - + -
601K ILE* 3.7 27.6 - - + -
602K ASP 3.4 13.7 - - - +
603K TYR* 4.2 7.0 - - + +
607K GLU* 1.3 69.9 - - - +
609K GLN* 1.3 61.4 + - - +
610K VAL* 3.9 14.7 + - + +
619K SER* 3.1 27.5 - - - -
620K ALA* 2.8 18.9 + - + +
621K GLN 3.7 12.3 - - - +
622K LYS* 4.3 6.1 - - - -
623K VAL* 4.0 15.7 - - + -
789K THR* 3.5 31.9 - - + -
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Residues in contact with GLN 609 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600K CYS* 3.8 1.6 - - - +
601K ILE* 3.6 2.8 - - - -
602K ASP* 2.8 54.6 + - + +
607K GLU* 3.2 30.2 + - - +
608K VAL* 1.3 73.2 - - - +
610K VAL* 1.3 61.9 + - - +
611K THR* 4.2 5.0 + - - +
618K TYR 3.6 3.4 - - - +
619K SER* 3.4 25.2 - - - -
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Residues in contact with VAL 610 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386K ILE* 3.9 21.1 - - + -
388K ILE* 4.8 0.7 - - + -
411K LEU* 3.8 15.3 - - + -
598K VAL* 3.6 37.5 - - + -
600K CYS 3.4 2.7 - - - -
601K ILE* 4.6 6.7 - - + -
608K VAL* 4.0 16.4 - - + -
609K GLN* 1.3 77.4 - - - +
611K THR* 1.3 65.6 + - - +
616K THR 3.7 0.9 - - - +
617K GLY* 3.6 1.7 - - - -
618K TYR* 2.7 50.2 + - + +
623K VAL* 4.2 16.2 - - + -
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Residues in contact with THR 611 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598K VAL* 3.9 0.6 - - - -
599K GLN* 2.9 22.7 + - - +
600K CYS* 3.0 35.1 + - - +
609K GLN* 4.9 5.0 + - - +
610K VAL* 1.3 79.0 + - - +
612K THR* 1.3 74.2 + - - +
615K GLY* 3.7 20.4 - - - +
616K THR 3.3 10.5 - - - +
617K GLY* 4.9 3.3 - - - +
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Residues in contact with THR 612 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411K LEU* 4.8 4.5 - - + -
596K SER* 4.1 26.5 - - - +
597K PRO* 3.1 18.6 - - - +
598K VAL* 4.8 2.5 - - - -
599K GLN* 4.1 7.8 - - - +
611K THR* 1.3 83.0 - - - +
613K THR* 1.3 60.5 + - - +
614K ASP* 2.6 30.4 + - - -
615K GLY* 3.0 15.8 + - - -
616K THR* 3.0 14.7 + - - +
618K TYR* 3.9 29.4 - - + -
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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