Contacts of the strand formed by residues 790 - 795 (chain A) in PDB entry 6F3T
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 790 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A SER* 3.5 37.7 - - - +
462A CYS* 3.7 15.0 - - - -
521A ASP* 4.5 6.3 - - - +
523A VAL* 4.3 15.7 - - + -
524A LEU* 4.1 33.0 - - + +
527A ILE* 4.0 22.2 - - + -
784A HIS 3.3 4.0 - - - +
785A PHE* 3.3 0.9 - - - -
786A THR* 2.8 42.7 + - + +
788A ARG* 3.3 3.0 - - + +
789A ASN* 1.3 76.9 - - - +
791A VAL* 1.3 62.5 + - - +
792A LEU* 4.3 4.7 - - + -
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Residues in contact with VAL 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A PRO* 3.9 7.0 - - + -
460A SER 2.8 19.1 + - - +
461A ILE* 3.6 34.5 - - + -
462A CYS* 2.7 36.2 + - - +
727A ALA* 5.6 2.7 - - + -
783A LEU* 4.0 27.8 - - + -
784A HIS 3.2 7.0 - - - +
785A PHE* 3.2 41.5 - - + -
790A LEU* 1.3 71.9 - - - +
792A LEU* 1.3 66.1 + - - +
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Residues in contact with LEU 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A CYS* 3.4 17.9 - - + +
464A TYR* 3.9 18.1 + - + +
478A VAL* 4.6 11.2 - - + -
482A SER* 5.0 5.6 - - - +
485A ILE* 4.7 14.1 - - + -
499A VAL* 6.0 4.0 - - + -
523A VAL* 5.1 5.6 - - + -
527A ILE* 4.5 14.8 - - + -
782A HIS* 3.7 3.3 + - - +
783A LEU* 3.6 3.3 - - - -
784A HIS* 2.8 63.4 + - + +
786A THR* 4.4 9.2 - - + -
790A LEU* 4.3 17.7 - - + -
791A VAL* 1.3 80.0 - - - +
793A ALA* 1.3 60.5 + - - +
794A ALA 4.0 0.2 + - - -
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Residues in contact with ALA 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ILE* 4.2 17.9 - - + -
462A CYS 2.8 13.2 + - - +
463A PHE* 3.3 10.4 - - + -
464A TYR* 2.9 30.2 + - - -
735A VAL* 4.8 1.8 - - + -
775A THR* 5.7 0.4 - - + -
780A VAL* 3.9 25.4 - - + -
782A HIS 3.6 4.9 - - - -
783A LEU* 3.9 11.9 - - + -
791A VAL 4.0 0.2 - - - -
792A LEU* 1.3 72.5 - - - +
794A ALA* 1.3 61.5 + - - +
795A GLY 3.5 0.9 + - - -
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Residues in contact with ALA 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A TYR* 3.3 34.9 - - + +
473A LEU* 5.0 2.7 - - + -
476A VAL* 4.0 17.3 - - + -
780A VAL* 3.2 3.5 - - - +
781A VAL* 2.8 29.3 + - + +
782A HIS* 2.9 31.1 + - + +
792A LEU 4.0 0.2 + - - -
793A ALA* 1.3 69.6 - - - +
795A GLY* 1.3 61.0 + - - +
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Residues in contact with GLY 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A PHE* 3.8 20.9 - - - -
464A TYR 2.8 16.0 + - - +
465A THR* 3.8 17.4 - - - -
466A PHE 4.1 0.9 + - - -
473A LEU* 3.4 15.5 - - - +
778A THR* 3.8 3.6 - - - -
779A PRO 3.3 9.6 - - - -
780A VAL* 4.2 0.4 - - - -
793A ALA 3.5 2.4 + - - -
794A ALA* 1.3 74.3 - - - +
796A ALA* 1.3 61.1 + - - -
797A TYR 3.7 3.5 + - - -
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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