Contacts of the strand formed by residues 778 - 785 (chain A) in PDB entry 6EJ9
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 VAL 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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736A ARG* 4.6 14.4 - - + +
772A TRP* 5.0 5.6 - - + -
776A PRO 3.5 4.2 + - - +
777A ASN* 1.3 77.8 - - - +
779A THR* 1.3 67.8 + - - +
780A VAL* 4.4 10.8 - - + -
798A LEU* 3.7 2.6 - - - +
799A ILE* 2.6 59.1 + - + +
827A HIS* 3.2 35.7 - - + +
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Residues in contact with THR 779 (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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778A VAL* 1.3 78.7 - - - +
780A VAL* 1.3 72.4 + - - +
796A ASP* 4.1 17.9 - - + +
797A ILE 3.4 19.1 - - - +
798A LEU* 3.6 19.3 - - + +
827A HIS* 3.0 28.1 + - - -
828A HIS* 5.0 8.2 + - + -
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Residues in contact with VAL 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A TRP* 4.0 31.4 - - + -
778A VAL* 4.4 13.0 - - + -
779A THR* 1.3 82.9 - - - +
781A THR* 1.3 64.7 + - - +
782A VAL* 4.9 1.8 - - + -
796A ASP* 3.2 7.2 - - - +
797A ILE* 3.1 53.1 + - + +
799A ILE* 4.3 2.5 - - + -
825A ILE* 3.9 16.6 - - + -
826A LEU 3.4 13.2 - - - +
827A HIS* 4.6 11.2 - - + +
828A HIS 5.9 0.4 - - - +
832A VAL* 5.5 3.6 - - + -
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Residues in contact with THR 781 (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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780A VAL* 1.3 75.1 - - - +
782A VAL* 1.3 64.4 + - - +
783A ILE* 4.3 11.0 - - + -
794A THR* 3.7 26.9 - - + -
795A TYR 3.6 0.9 - - - +
796A ASP* 2.8 25.2 + - - +
824A LYS 3.6 0.9 - - - +
825A ILE* 3.2 7.3 - - - +
826A LEU* 2.8 48.5 + - + +
828A HIS* 5.1 6.1 + - - -
829A TRP 5.8 0.6 + - - -
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Residues in contact with VAL 782 (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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770A GLN* 4.7 13.9 - - - +
780A VAL* 4.9 2.2 - - + -
781A THR* 1.3 73.8 - - - +
783A ILE* 1.3 66.8 + - - +
784A TRP* 3.7 15.0 - - + +
794A THR* 3.3 8.7 - - - +
795A TYR* 2.9 64.0 + - + +
797A ILE* 3.7 31.0 - - + -
823A VAL* 3.9 17.9 - - + -
824A LYS 3.3 4.3 - - - +
825A ILE* 4.7 10.3 - - + -
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Residues in contact with ILE 783 (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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781A THR* 4.3 6.5 - - + -
782A VAL* 1.3 81.6 - - - +
784A TRP* 1.3 65.3 + - - +
785A VAL* 4.0 17.0 - - + +
791A ILE* 4.0 24.7 - - + -
793A ALA 3.6 3.1 - - - +
794A THR* 4.0 15.9 - - + +
822A THR 3.8 0.5 - - - +
823A VAL* 3.3 5.4 - - - +
824A LYS* 2.8 50.0 + - + +
826A LEU* 3.3 35.2 - - + -
875A LEU* 5.0 2.9 - - + -
879A LEU* 3.7 29.4 - - + -
881A LEU* 5.4 0.4 - - + -
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Residues in contact with TRP 784 (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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742A VAL* 4.2 6.7 - - + -
766A PRO* 3.9 29.2 - - + -
767A VAL 4.1 2.9 - - - -
768A GLY* 3.8 32.3 - - - -
782A VAL* 3.7 13.9 - - + +
783A ILE* 1.3 78.6 - - - +
785A VAL* 1.3 61.2 + - - +
791A ILE* 3.6 5.9 - - - +
792A ALA* 2.9 36.1 + - + -
793A ALA* 3.1 24.0 + - + +
795A TYR* 3.2 32.5 + + - -
810A PRO* 3.7 30.7 - - + -
812A LEU* 4.4 12.3 - - + -
821A TRP* 4.6 6.3 - + + -
822A THR 3.6 4.0 - - - -
823A VAL* 3.9 18.4 - - + +
837A PHE* 3.9 22.2 - + - -
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Residues in contact with VAL 785 (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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783A ILE* 4.0 17.7 - - + +
784A TRP* 1.3 78.6 - - - +
786A ASP* 1.3 65.6 + - - +
789A ASN* 3.7 38.6 - - - +
790A VAL 3.6 2.9 - - - +
791A ILE* 4.7 3.1 - - + -
821A TRP* 3.4 10.4 - - - -
822A THR* 2.8 50.8 + - - +
824A LYS* 4.9 10.3 - - + -
881A LEU* 3.9 30.1 - - + -
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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