Contacts of the strand formed by residues 706 - 712 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544B MSE 3.6 5.5 - - - +
588B LEU* 2.9 50.7 + - + +
602B LEU* 4.6 10.3 - - + -
615B ILE* 3.6 36.6 - - + -
617B GLN 3.8 11.2 - - - +
618B GLY* 4.9 1.1 - - - -
619B LYS 3.6 20.2 - - - +
620B VAL* 4.8 1.3 - - + -
702B ALA* 3.5 26.0 - - + -
704B VAL 2.8 28.7 + - - +
705B ASP* 1.3 77.1 - - - +
707B GLN* 1.3 70.9 + - - +
708B TYR* 4.6 6.3 - - + -
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Residues in contact with GLN 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B MSE 3.4 40.2 + - + +
545B LYS* 4.2 5.3 - - - +
546B ILE* 3.3 27.1 - - + +
585B ILE* 5.8 6.4 - - + +
586B GLN 4.0 5.3 + - - +
587B GLU* 3.5 25.5 + - - +
615B ILE* 3.9 1.9 - - - +
616B LEU* 2.9 33.7 + - + -
617B GLN* 3.1 45.2 + - + +
706B LEU* 1.3 77.0 - - - +
708B TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585B ILE* 3.7 3.7 - - - +
586B GLN* 2.7 69.3 + - + +
587B GLU 4.9 0.7 - - - -
588B LEU* 4.0 31.2 - - + +
602B LEU* 3.8 27.7 - - + +
613B ILE* 3.7 29.2 - - + -
614B LEU 3.3 15.3 - - - +
615B ILE* 4.2 12.8 - - + -
616B LEU* 4.2 3.7 - - - +
706B LEU* 4.6 6.1 - - + -
707B GLN* 1.3 77.0 - - - +
709B ILE* 1.3 67.0 + - - +
710B LYS* 4.0 24.3 + - + -
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Residues in contact with ILE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B LEU* 5.7 6.5 - - + -
554B ALA* 6.0 1.8 - - + -
558B LEU* 4.3 16.4 - - + -
579B LEU* 4.4 15.5 - - + -
584B VAL* 3.2 14.1 - - + +
585B ILE* 4.6 13.9 - - + -
612B PHE* 3.8 1.7 - - + +
613B ILE* 3.1 8.3 - - - +
614B LEU* 2.9 55.3 + - + +
616B LEU* 3.6 32.3 - - + -
708B TYR* 1.3 79.2 - - - +
710B LYS* 1.3 59.6 + - - +
711B ILE* 4.1 24.7 - - + -
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B ASP 4.4 3.3 - - - +
584B VAL* 2.7 38.8 + - - +
586B GLN* 3.7 25.3 - - + +
611B TYR* 3.8 48.0 - - + -
612B PHE 3.5 2.7 - - - -
613B ILE* 3.9 5.4 - - + -
708B TYR* 4.0 27.6 + - + -
709B ILE* 1.3 72.9 - - - +
711B ILE* 1.3 65.7 + - - +
712B THR* 4.2 10.1 - - + -
715B GLN* 4.0 3.3 - - - +
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Residues in contact with ILE 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558B LEU* 4.8 1.3 - - + -
565B PHE* 4.3 22.0 - - + -
575B LEU* 5.5 0.4 - - + -
578B LEU* 3.8 35.0 - - + -
579B LEU* 4.3 11.9 - - + -
584B VAL* 4.4 9.0 - - + -
611B TYR* 4.4 0.7 - - - -
612B PHE* 2.9 48.5 + - + +
644B LEU* 3.5 9.6 - - + +
709B ILE* 4.1 22.4 - - + -
710B LYS* 1.3 79.2 - - - +
712B THR* 1.3 74.0 + - - +
715B GLN* 3.7 8.7 - - + -
716B TYR* 4.3 13.2 - - + +
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Residues in contact with THR 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ASP* 3.9 21.1 - - - +
611B TYR* 4.1 13.9 - - + +
644B LEU* 3.6 7.1 - - - +
710B LYS* 4.7 11.9 - - + -
711B ILE* 1.3 79.0 - - - +
713B ARG* 1.3 64.8 + - - +
714B GLN* 3.8 7.3 + - - +
715B GLN* 3.0 35.5 + - - +
716B TYR 3.3 15.9 + - - -
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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