Contacts of the strand formed by residues 830 - 839 (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 830 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826A LEU* 3.3 2.5 - - - -
827A HIS* 2.8 46.9 + - + +
828A HIS* 4.0 7.2 - - + +
829A TRP* 1.3 77.8 - - - +
831A PRO* 1.3 82.4 - - + +
832A VAL* 3.7 2.2 - - + +
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Residues in contact with PRO 831 (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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826A LEU* 3.8 16.1 - - + -
829A TRP 3.3 9.6 - - - +
830A VAL* 1.3 98.5 - - + +
832A VAL* 1.3 62.9 + - - +
833A ALA 5.5 0.2 - - - +
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Residues in contact with VAL 832 (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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727A ILE* 3.2 30.6 - - + +
737A LEU* 3.7 32.1 - - + -
772A TRP* 6.1 0.7 - - + -
780A VAL* 5.5 3.4 - - + -
825A ILE* 2.9 23.1 + - + +
826A LEU 4.0 1.6 - - - -
827A HIS* 3.7 27.1 - - + +
830A VAL* 3.7 10.3 - - + +
831A PRO* 1.3 80.4 - - - +
833A ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 833 (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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725A PHE* 3.8 16.4 - - + -
726A LYS 3.3 14.4 - - - +
727A ILE* 3.9 8.5 - - + -
737A LEU* 3.5 27.6 - - + -
740A SER* 5.8 0.2 - - - -
824A LYS* 3.8 1.4 - - - +
825A ILE* 3.0 30.9 + - + +
832A VAL* 1.3 80.8 - - - +
834A GLU* 1.3 67.0 + - - +
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Residues in contact with GLU 834 (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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724A VAL 3.6 2.8 - - - +
725A PHE* 3.5 6.5 - - - -
726A LYS* 3.0 50.2 + - + +
740A SER* 5.6 1.3 - - - -
822A THR* 3.9 11.2 - - + +
823A VAL 3.2 13.7 - - - +
824A LYS* 3.4 32.5 - - + -
825A ILE* 5.9 0.9 - - - -
833A ALA* 1.3 77.3 - - - +
835A THR* 1.3 63.6 + - - +
836A LYS* 4.2 20.1 + - - +
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Residues in contact with THR 835 (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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724A VAL* 3.6 21.1 + - - +
725A PHE* 4.3 6.1 + - - +
740A SER* 3.7 41.1 + - - +
741A GLU* 4.4 5.3 - - - +
742A VAL* 4.5 13.5 + - + -
822A THR* 3.5 5.6 - - - +
823A VAL* 2.8 48.8 + - + +
834A GLU* 1.3 75.1 - - - +
836A LYS* 1.3 77.3 + - - +
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Residues in contact with LYS 836 (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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724A VAL* 3.5 44.2 - - + +
742A VAL* 5.5 1.2 + - - +
820A VAL* 4.0 20.9 - - + +
821A TRP 3.3 14.4 - - - +
822A THR* 3.4 21.2 + - + +
834A GLU* 4.2 19.3 + - - +
835A THR* 1.3 86.1 + - - +
837A PHE* 1.3 67.5 + - - +
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Residues in contact with PHE 837 (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* 3.6 42.0 - - + +
758A GLY 6.0 1.3 - - - +
760A LEU* 3.9 24.7 - - + -
766A PRO* 4.4 8.5 - - + -
784A TRP* 3.9 24.9 - + - -
816A LEU* 5.9 0.2 - - + -
820A VAL* 3.6 5.1 - - - -
821A TRP* 2.9 63.8 + + + +
823A VAL* 3.9 13.9 - - + -
835A THR 5.5 0.2 - - - -
836A LYS* 1.3 79.1 - - - +
838A LEU* 1.3 61.1 + - - +
839A VAL* 3.6 26.5 - - + -
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Residues in contact with LEU 838 (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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651A LEU* 4.9 10.8 - - + -
758A GLY 4.5 6.7 + - - +
760A LEU* 3.6 23.9 + - - +
819A GLY* 3.6 25.4 - - - +
820A VAL* 4.3 13.5 - - + +
837A PHE* 1.3 75.1 - - - +
839A VAL* 1.3 74.0 + - - +
840A ALA* 3.8 17.8 + - + +
841A PRO* 5.5 2.7 - - + -
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Residues in contact with VAL 839 (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 LEU* 3.9 8.7 - - + -
761A GLY 3.7 26.9 - - - +
762A PRO* 3.8 11.4 - - + -
816A LEU* 4.2 20.2 - - + +
817A ARG 4.1 4.3 - - - +
818A PRO* 3.3 14.7 - - + +
819A GLY 2.8 38.6 + - - +
821A TRP* 3.7 18.2 - - - +
837A PHE* 3.6 27.3 + - + -
838A LEU* 1.3 72.5 - - - +
840A ALA* 1.3 63.8 + - - +
841A PRO* 4.0 0.2 - - - +
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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