Contacts of the strand formed by residues 787 - 791 (chain A) in PDB entry 1FO4
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 ILE 787 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A GLY 4.1 5.4 - - - +
760A MET* 3.5 19.5 - - + -
762A LEU* 3.7 22.9 - - + -
773A GLN* 2.8 61.8 + - + +
776A VAL* 4.1 16.6 - - + -
777A ALA* 3.9 27.1 - - + +
780A LEU* 4.1 3.4 - - + -
782A VAL* 4.1 16.8 - - + -
783A PRO 4.4 2.9 - - - +
784A VAL 3.1 3.1 + - - +
785A ASN 4.7 1.8 - - - +
786A ARG* 1.3 86.4 - - - +
788A LEU* 1.3 62.0 + - - +
789A VAL* 4.1 3.4 - - + -
1068A THR* 3.6 0.7 + - - -
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Residues in contact with LEU 788 (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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760A MET 2.9 13.9 + - - +
761A GLU* 3.4 34.7 - - + +
762A LEU* 2.8 29.8 + - - +
786A ARG 3.9 1.1 + - - +
787A ILE* 1.3 73.9 - - - +
789A VAL* 1.3 68.8 + - - +
790A ARG* 4.0 18.4 - - + -
1067A SER* 4.2 0.2 - - - -
1068A THR* 3.5 14.4 - - - +
1069A ASN* 3.6 44.9 - - + +
790B ARG* 4.3 8.5 - - - +
1065B GLU* 5.4 0.9 - - - +
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Residues in contact with VAL 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A LEU* 3.6 8.3 - - + -
764A VAL* 4.0 18.8 - - + -
766A THR* 4.7 0.4 - - + -
769A ALA* 4.0 25.2 - - + +
772A THR* 3.8 23.3 - - + -
773A GLN* 3.6 36.8 - - + +
787A ILE* 4.1 7.0 - - + -
788A LEU* 1.3 78.8 - - - +
790A ARG* 1.3 62.4 + - - +
791A VAL* 4.5 5.8 - - + -
1066A THR 4.0 0.2 - - - +
1067A SER* 3.2 4.7 - - - -
1068A THR* 3.0 36.5 + - + +
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Residues in contact with ARG 790 (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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761A GLU* 2.7 44.2 + - - -
762A LEU 2.9 10.2 + - - +
763A PHE* 3.4 34.2 - - + +
764A VAL 3.2 23.4 + - - -
788A LEU* 4.0 15.7 - - + +
789A VAL* 1.3 79.0 - - - +
791A VAL* 1.3 62.4 + - - +
792A LYS 4.1 1.2 + - - -
1065A GLU* 2.9 40.1 + - - +
1066A THR 3.3 4.9 - - - +
1067A SER* 3.9 11.0 - - - -
754B LYS* 4.7 3.4 - - - +
761B GLU* 2.9 39.4 + - - -
788B LEU* 4.4 9.2 - - - +
790B ARG* 3.3 6.2 - - - +
1069B ASN* 6.0 0.2 - - - +
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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
----------------------------------------------------------
764A VAL 3.4 22.9 - - - +
766A THR* 3.6 41.3 - - + +
769A ALA* 4.4 14.1 - - + -
789A VAL* 4.5 2.7 - - + -
790A ARG* 1.3 76.9 - - - +
792A LYS* 1.3 64.4 + - - +
793A ARG* 4.0 18.4 - - - +
794A MET* 4.6 1.3 - - + -
1036A THR* 4.0 25.8 - - + -
1065A GLU* 4.3 1.6 - - - -
1066A THR* 2.8 35.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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