Contacts of the strand formed by residues 825 - 830 (chain B) in PDB entry 6FF7
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 PRO 825 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B GLU* 6.1 2.2 - - + -
665B THR 3.4 15.5 - - - +
666B VAL* 4.2 7.0 - - + -
820B PHE* 4.3 15.5 - - + +
821B LEU* 4.6 12.6 - - + +
823B ALA 3.7 1.0 - - - -
824B THR* 1.3 79.1 - - - +
826B ARG* 1.3 62.8 + - - +
910B ASP* 4.8 7.8 - - - +
911B PRO* 4.5 15.8 - - + +
912B LEU* 5.6 1.2 + - - +
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Residues in contact with ARG 826 (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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664B GLU* 3.6 4.9 - - - +
665B THR* 2.9 36.9 + - - +
666B VAL* 4.4 0.6 - - - +
667B VAL* 5.2 14.1 - - + -
824B THR 5.2 0.2 - - - +
825B PRO* 1.3 76.4 - - - +
827B LEU* 1.3 67.5 + - - +
906B ILE* 5.8 6.1 - - + -
907B VAL 5.9 1.8 - - - +
909B GLY 4.8 11.7 - - - +
910B ASP* 5.8 0.7 - - - -
911B PRO* 5.5 5.6 - - - -
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Residues in contact with LEU 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B PHE* 5.9 3.6 - - + -
663B CYS 3.5 10.3 - - - +
664B GLU* 4.4 1.3 - - - +
665B THR* 5.8 1.2 - - - -
826B ARG* 1.3 81.0 - - - +
828B MET* 1.3 63.2 + - - +
829B GLU 4.3 0.2 - - - -
906B ILE* 3.9 4.9 - - - +
907B VAL* 3.4 31.4 + - + +
909B GLY 5.0 4.0 + - - -
911B PRO* 5.8 8.2 - - + +
930B ALA* 5.1 10.7 - - + +
934B MET* 6.6 0.2 - - + -
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Residues in contact with MET 828 (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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662B PHE* 3.4 9.4 - - - +
663B CYS* 2.8 48.0 + - + +
664B GLU* 4.7 4.9 - - - +
665B THR* 5.4 5.8 - - - -
827B LEU* 1.3 74.6 - - - +
829B GLU* 1.3 59.2 + - - +
904B TRP* 3.9 22.4 - - + -
905B GLN 3.0 15.0 - - - +
906B ILE* 5.2 0.2 - - - -
907B VAL* 5.4 0.2 - - - -
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Residues in contact with GLU 829 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B PHE* 4.7 7.0 - - + -
828B MET* 1.3 74.5 - - - +
830B PRO* 1.3 68.0 - - - +
831B TYR 3.9 0.2 + - - -
876B PRO* 6.0 4.9 - - + -
877B ALA 6.1 0.2 - - - +
878B ILE* 6.5 1.3 - - + -
904B TRP* 3.7 2.8 - - - -
905B GLN* 2.9 34.5 + - + +
906B ILE 5.9 0.2 - - - -
907B VAL* 4.8 14.3 - - + +
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Residues in contact with PRO 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B VAL* 5.0 13.7 - - + -
660B VAL* 5.6 3.3 - - + -
661B THR 4.9 12.5 - - - +
828B MET 4.3 0.4 - - - -
829B GLU* 1.3 79.0 - - - +
831B TYR* 1.3 64.4 + - - +
876B PRO* 3.9 3.5 - - - +
877B ALA* 3.1 33.8 + - + +
901B PHE* 6.4 1.3 - - + -
902B HIS 4.7 6.7 - - - +
903B HIS 4.5 5.6 - - - +
904B TRP* 4.8 3.1 - - + -
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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