Contacts of the strand formed by residues 781 - 790 (chain A) in PDB entry 5ES4
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 GLU 781 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A LEU* 5.9 2.4 - - - +
779A ASN* 4.6 9.4 - - - +
780A LEU* 1.3 80.9 + - + +
782A LEU* 1.3 63.0 + - - +
783A ASN* 3.3 29.9 + - - +
811A ARG* 2.6 43.3 + - - +
813A VAL* 5.9 0.2 - - - +
862A THR* 3.8 8.2 - - + +
863A PHE 3.3 5.6 - - - +
864A ASP* 4.3 0.4 - - - +
865A VAL* 4.1 3.1 - - - -
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Residues in contact with LEU 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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768A PHE* 3.8 32.3 - - + -
771A LEU* 3.4 33.0 - - + -
774A LEU* 4.6 16.2 - - + -
779A ASN* 6.2 1.1 - - + -
781A GLU* 1.3 76.5 - - - +
783A ASN* 1.3 62.1 + - - +
784A ALA 3.7 1.1 + - - -
808A LEU* 3.8 23.6 - - + -
861A ALA 3.7 0.5 - - - +
862A THR* 3.1 6.4 - - - -
863A PHE* 2.8 48.1 + - + +
865A VAL* 4.0 10.3 - - + -
875A LEU* 4.0 19.1 - - + -
877A LEU* 5.4 2.0 - - + -
899A LEU* 5.9 1.6 - - + -
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Residues in contact with ASN 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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768A PHE* 3.2 15.8 - - - +
769A PRO* 3.3 27.7 - - + +
771A LEU* 5.6 6.4 - - + +
781A GLU* 3.3 27.2 + - - +
782A LEU* 1.3 75.7 - - - +
784A ALA* 1.3 59.9 + - - +
860A LEU* 5.8 3.8 - - + -
861A ALA 4.1 1.1 - - - -
862A THR* 2.7 36.8 + - - +
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Residues in contact with ALA 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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766A PHE* 5.0 6.5 - - + -
767A SER 3.5 6.5 - - - +
768A PHE* 3.6 18.8 - - + -
782A LEU 3.7 1.0 + - - -
783A ASN* 1.3 71.6 - - - +
785A GLU* 1.3 59.4 + - - +
786A VAL* 3.7 11.4 + - + -
802A PHE* 5.1 2.7 - - + -
860A LEU* 3.4 6.9 - - - +
861A ALA* 2.8 55.1 + - + +
863A PHE* 4.3 11.7 - - + -
877A LEU* 5.4 1.3 - - + -
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Residues in contact with GLU 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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766A PHE* 3.1 2.6 - - - -
767A SER* 2.9 54.1 + - - +
769A PRO* 4.3 18.5 - - + +
783A ASN 3.8 1.4 + - - -
784A ALA* 1.3 70.9 - - - +
786A VAL* 1.3 61.7 + - - +
787A MET* 3.8 2.1 + - + +
822A LEU* 5.9 2.6 - - - +
858A THR* 3.8 22.7 - - + +
860A LEU* 3.7 21.4 - - + +
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Residues in contact with VAL 786 (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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764A ILE* 3.6 35.7 - - + -
766A PHE* 3.6 21.3 - - + -
784A ALA* 4.3 11.4 - - + +
785A GLU* 1.3 72.5 - - - +
787A MET* 1.3 63.3 + - - +
800A ILE* 4.3 2.5 - - + -
802A PHE* 3.8 28.9 - - + -
857A ILE 4.0 0.2 - - - +
858A THR* 3.2 4.3 - - - -
859A PHE* 2.9 68.4 + - + +
861A ALA* 4.6 2.7 - - + -
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Residues in contact with MET 787 (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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764A ILE* 3.5 3.8 - - - +
765A SER* 2.8 52.0 + - - +
785A GLU* 3.8 2.7 + - + +
786A VAL* 1.3 73.6 - - - +
788A VAL* 1.3 62.9 + - - +
789A TRP* 3.6 29.1 - - + -
856A GLN* 4.4 22.0 - - - +
857A ILE 4.6 0.7 - - - +
858A THR* 3.5 26.0 - - + +
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Residues in contact with VAL 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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762A LEU* 5.2 0.2 - - + -
763A GLY 3.1 19.7 - - - +
764A ILE* 3.8 13.9 - - + -
786A VAL* 4.9 0.9 - - + -
787A MET* 1.3 74.9 - - - +
789A TRP* 1.3 66.0 + - - +
798A THR* 5.5 1.3 - - + -
800A ILE* 4.2 17.0 - - + -
846A ILE* 5.0 4.0 - - + -
851A PHE* 3.4 10.6 - - + -
856A GLN* 3.5 2.7 - - - +
857A ILE* 2.8 60.3 + - + +
859A PHE* 5.3 3.4 - - + -
881A VAL* 3.5 32.3 - - + -
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Residues in contact with TRP 789 (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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762A LEU* 3.6 5.9 - - - +
763A GLY* 2.9 63.8 + - - +
764A ILE 3.3 35.2 - - - -
765A SER* 3.5 17.9 - - - -
787A MET* 3.6 26.7 - - + -
788A VAL* 1.3 81.4 - - - +
790A ASN* 1.3 59.1 + - - +
791A ASP* 3.6 30.2 + - + +
851A PHE* 3.5 8.7 - - - -
855A ALA 4.5 0.7 - - - +
856A GLN* 3.8 20.9 - - + +
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Residues in contact with ASN 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 ASN 2.9 18.7 + - - +
762A LEU* 3.4 16.3 - - - +
789A TRP* 1.3 71.5 - - - +
791A ASP* 1.3 68.8 + - - +
792A GLY 3.1 10.9 + - - -
793A GLU 2.6 27.0 + - - +
795A SER 3.7 3.4 - - - +
851A PHE* 2.7 35.0 + - + -
852A ARG 3.3 15.7 - - - +
853A GLY* 2.9 25.5 - - - +
854A GLY* 3.6 8.3 - - - -
855A ALA 3.0 10.4 + - - +
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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
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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