Contacts of the strand formed by residues 706 - 712 (chain D) in PDB entry 6G52
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 LEU 706 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587D GLU* 3.9 0.5 - - - +
588D LEU* 2.8 52.4 + - + +
602D LEU* 5.8 5.8 - - + -
615D ILE* 4.9 10.1 - - + -
617D GLN* 3.2 15.3 - - - +
618D GLY* 4.2 4.3 - - - -
619D LYS 3.9 10.1 - - - +
620D VAL* 4.3 13.7 - - + -
702D ALA* 3.4 34.8 - - + -
704D VAL 3.2 8.5 + - - +
705D ASP* 1.3 73.9 - - - +
707D GLN* 1.3 57.0 + - - +
708D TYR* 3.3 42.2 - - + -
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Residues in contact with GLN 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D ILE* 5.9 2.9 - - + -
586D GLN 3.7 6.1 - - - +
587D GLU* 4.1 15.5 - - + +
615D ILE* 3.8 0.4 - - - -
616D LEU* 2.8 42.5 + - + +
617D GLN* 3.1 24.7 + - + +
706D LEU* 1.3 75.1 - - - +
708D TYR* 1.3 53.5 + - - +
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Residues in contact with TYR 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D ILE* 3.7 4.0 - - - +
586D GLN* 2.8 60.8 + - + +
587D GLU 5.0 0.2 - - - -
588D LEU* 4.2 20.6 - - + +
602D LEU* 5.5 8.7 - - + +
611D TYR* 5.8 0.2 - + - -
613D ILE* 3.5 35.7 - - + -
614D LEU 3.4 13.7 - - - +
615D ILE* 3.9 18.8 - - + -
616D LEU* 4.0 1.8 - - - +
706D LEU* 3.3 28.5 - - + -
707D GLN* 1.3 75.0 - - - +
709D ILE* 1.3 65.7 + - - +
710D LYS* 4.1 21.7 + - + -
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Residues in contact with ILE 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554D ALA* 5.9 1.8 - - + -
558D LEU* 3.6 31.9 - - + -
579D LEU* 3.6 19.5 - - + -
584D VAL* 3.2 8.7 - - + +
585D ILE* 3.8 19.1 - - + -
612D PHE* 3.7 1.6 - - + +
613D ILE* 2.9 7.8 - - - +
614D LEU* 2.9 53.6 + - + +
616D LEU* 3.6 34.5 - - + -
708D TYR* 1.3 75.8 - - - +
710D LYS* 1.3 59.6 + - - +
711D ILE* 3.8 15.9 - - + -
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Residues in contact with LYS 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D ASP 4.3 8.3 - - - +
584D VAL* 2.5 32.6 + - - +
586D GLN* 5.5 4.5 - - + -
611D TYR* 3.5 53.8 - - + -
612D PHE 3.5 2.9 - - - -
613D ILE* 3.6 6.5 - - + -
708D TYR* 4.1 25.6 + - + -
709D ILE* 1.3 73.2 - - - +
711D ILE* 1.3 63.6 + - - +
712D THR* 4.2 11.3 + - + +
715D GLN* 3.9 4.7 + - - +
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Residues in contact with ILE 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558D LEU* 4.6 2.2 - - + -
565D PHE* 3.5 35.9 - - + -
578D LEU* 3.8 31.0 - - + -
579D LEU* 4.7 4.5 - - + -
584D VAL* 5.0 5.2 - - + -
611D TYR* 4.1 0.7 - - - -
612D PHE* 2.9 41.9 + - + +
644D LEU* 3.3 9.4 - - + +
709D ILE* 3.8 28.7 - - + -
710D LYS* 1.3 77.5 - - - +
712D THR* 1.3 69.2 + - - +
715D GLN* 4.0 6.7 - - - +
716D TYR* 4.1 20.0 - - + +
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Residues in contact with THR 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610D ASP* 4.0 15.0 - - - +
611D TYR* 3.8 22.2 - - + -
644D LEU* 3.9 2.9 - - - -
710D LYS* 4.5 14.6 - - + +
711D ILE* 1.3 77.4 - - - +
713D ARG* 1.3 64.9 + - - +
714D GLN* 3.8 6.9 + - - +
715D GLN* 3.2 34.1 + - - +
716D TYR* 3.1 22.9 + - - +
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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