Contacts of the strand formed by residues 796 - 804 (chain v) 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 ASN 796 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790v ILE* 4.0 3.8 - - - -
791v HIS* 3.2 34.4 + - + +
794v SER 3.2 9.2 + - - +
795v ASN* 1.3 75.5 - - - +
797v LEU* 1.3 64.3 + - - +
868v VAL* 5.9 2.0 - - + -
869v MET 3.6 15.3 - - - +
870v ASN* 4.9 4.3 - - + +
871v PRO* 5.0 4.7 - - - -
934v GLY* 4.8 14.8 - - - +
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Residues in contact with LEU 797 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788v PHE* 5.0 7.4 - - + -
789v VAL 3.8 11.2 - - - +
796v ASN* 1.3 78.2 - - - +
798v ILE* 1.3 60.9 + - - +
799v ILE* 4.1 3.1 - - + +
867v ARG 3.7 0.7 - - - +
868v VAL* 3.2 5.4 - - - +
869v MET* 2.9 44.4 + - + +
871v PRO* 5.3 9.4 - - + -
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Residues in contact with ILE 798 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787v LYS 4.3 0.2 - - - +
788v PHE* 3.3 19.8 - - - -
789v VAL* 3.4 17.8 + - + +
797v LEU* 1.3 73.3 - - - +
799v ILE* 1.3 60.7 + - - +
867v ARG 3.6 4.9 - - - -
868v VAL* 4.5 7.4 - - + +
891v VAL* 5.1 10.6 - - + +
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Residues in contact with ILE 799 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785v PRO* 5.7 8.3 - - + -
787v LYS 3.6 6.3 - - - +
788v PHE* 3.8 11.9 - - + -
797v LEU* 5.5 3.1 - - + -
798v ILE* 1.3 75.0 - - - +
800v ILE* 1.3 62.9 + - - +
801v GLU* 5.7 0.2 - - - -
866v ILE* 3.5 5.4 - - - +
867v ARG* 2.9 44.3 + - + +
891v VAL* 6.0 0.9 - - - -
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Residues in contact with ILE 800 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784v THR 3.6 0.2 - - - +
785v PRO* 3.6 4.7 - - - +
786v ARG* 3.0 36.8 + - + +
787v LYS 3.2 12.5 + - - +
799v ILE* 1.3 75.9 - - - +
801v GLU* 1.3 60.5 + - - +
802v THR* 4.2 0.7 - - - -
865v VAL 3.8 4.0 - - - +
866v ILE* 4.7 3.1 - - + +
888v ALA* 4.0 27.6 - - + +
889v PHE 5.4 0.9 - - - +
890v SER 5.7 3.1 - - - +
891v VAL* 5.0 15.5 - - + +
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Residues in contact with GLU 801 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781v LEU* 6.3 1.6 - - + -
782v GLN* 5.9 2.0 - - + +
783v TYR* 3.7 29.1 - - + +
784v THR 3.3 7.0 - - - +
785v PRO* 4.7 2.0 - - + -
799v ILE 5.6 0.4 - - - +
800v ILE* 1.3 73.8 - - - +
802v THR* 1.3 60.4 + - - +
864v SER* 2.9 27.9 - - - -
865v VAL* 2.9 26.7 + - + +
867v ARG* 6.1 4.3 - - + -
888v ALA* 5.4 0.4 - - - +
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Residues in contact with THR 802 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783v TYR* 3.9 1.4 - - - +
784v THR* 3.0 30.7 + - - +
786v ARG* 5.1 8.2 - - - +
800v ILE 4.2 0.4 - - - -
801v GLU* 1.3 74.6 - - - +
803v ASP* 1.3 59.6 + - - +
804v HIS 4.3 0.2 - - - -
863v ALA 3.3 7.4 - - - -
864v SER* 4.3 6.3 - - - -
887v ALA* 4.8 6.7 - - - -
888v ALA* 3.6 25.8 - - - -
56x ALA 5.2 1.6 - - - +
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Residues in contact with ASP 803 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430v GLY* 5.6 6.1 - - - -
783v TYR* 4.4 15.3 - - + +
784v THR* 4.8 5.8 - - - +
802v THR* 1.3 75.0 - - - +
804v HIS* 1.3 66.7 + - - +
805v ASN 3.9 0.2 + - - -
806v ALA* 3.8 23.2 - - + +
862v TRP* 3.6 2.3 - - - -
863v ALA* 2.9 36.1 + - + +
56x ALA 4.8 2.7 - - - +
58x ASN* 5.6 5.8 - - + -
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Residues in contact with HIS 804 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803v ASP* 1.3 73.5 - - - +
805v ASN* 1.3 74.4 + - + +
861v GLN 3.5 9.2 - - - +
862v TRP* 4.6 2.9 - - + +
56x ALA* 3.7 21.8 + - + +
57x GLU* 4.4 7.6 - - + -
58x ASN* 3.8 19.6 + - - +
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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