Contacts of the strand formed by residues 819 - 827 (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 GLY 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787A PRO* 3.6 8.3 - - - -
818A PRO* 1.3 74.8 - - - +
820A VAL* 1.3 63.7 + - - -
821A TRP* 3.5 5.2 + - - -
838A LEU* 3.6 10.9 - - - +
839A VAL 2.8 32.9 + - - -
841A PRO* 5.1 2.1 - - - +
905A TRP* 5.6 4.3 - - - -
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Residues in contact with VAL 820 (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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786A ASP 4.4 0.9 - - - +
787A PRO* 3.5 21.2 - - - +
819A GLY* 1.3 72.1 - - - -
821A TRP* 1.3 72.7 + - - +
822A THR* 4.7 2.6 + - - +
836A LYS* 4.0 28.5 - - + +
837A PHE 3.6 9.0 - - - +
838A LEU* 4.3 15.5 - - + +
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Residues in contact with TRP 821 (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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784A TRP* 4.6 8.5 - + + -
785A VAL 3.4 20.9 - - - -
786A ASP* 3.6 18.8 - - + +
787A PRO* 3.3 10.0 - - + +
792A ALA* 3.9 17.7 - - + -
812A LEU* 4.4 11.2 - - + -
816A LEU* 3.9 22.7 - - + -
817A ARG 3.0 20.5 + - - -
819A GLY 3.6 13.0 - - - -
820A VAL* 1.3 75.2 - - - +
822A THR* 1.3 65.0 + - - +
836A LYS* 3.3 8.1 - - - +
837A PHE* 2.9 65.0 + + + -
839A VAL* 3.7 19.0 - - + +
867A TYR* 3.5 46.7 - + - -
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Residues in contact with THR 822 (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 3.8 0.5 - - - +
784A TRP* 3.6 2.6 - - - +
785A VAL* 2.8 46.6 + - - +
820A VAL* 4.7 3.1 + - - +
821A TRP* 1.3 76.4 + - - +
823A VAL* 1.3 73.7 + - - +
824A LYS* 4.2 14.1 - - + -
834A GLU* 3.9 22.9 - - - +
835A THR 3.5 11.4 - - - +
836A LYS* 3.4 25.6 + - - +
837A PHE* 5.2 0.2 - - - -
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Residues in contact with VAL 823 (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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740A SER* 5.1 5.4 - - - +
742A VAL* 3.7 26.5 - - + -
768A GLY* 6.1 1.6 - - - -
770A GLN* 5.7 4.3 - - - +
782A VAL* 3.9 22.4 - - + -
783A ILE 3.3 8.5 - - - +
784A TRP* 3.9 22.0 - - + +
822A THR* 1.3 78.3 - - - +
824A LYS* 1.3 64.2 + - - +
825A ILE* 5.3 4.3 - - + +
834A GLU* 3.2 5.0 - - - +
835A THR* 2.8 46.9 + - + +
837A PHE* 3.9 15.5 - - + -
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Residues in contact with LYS 824 (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 3.6 0.9 - - - +
782A VAL* 3.3 6.6 - - - +
783A ILE* 2.8 48.0 + - + +
785A VAL* 4.9 11.7 - - + -
822A THR* 4.3 12.8 - - + -
823A VAL* 1.3 75.5 - - - +
825A ILE* 1.3 64.4 + - - +
826A LEU* 4.9 13.5 - - + -
833A ALA 3.8 3.1 - - - +
834A GLU* 3.4 31.4 - - + +
879A LEU* 4.7 12.8 + - + +
880A SER 5.5 0.2 + - - -
881A LEU* 4.0 31.2 - - + +
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Residues in contact with ILE 825 (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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737A LEU* 3.8 22.9 - - + -
740A SER* 4.1 16.4 - - - +
770A GLN* 3.8 28.9 - - + +
772A TRP* 4.9 3.8 - - + -
780A VAL* 3.9 27.8 - - + -
781A THR 3.2 8.5 - - - +
782A VAL* 4.7 12.3 - - + -
823A VAL* 5.3 4.5 - - + +
824A LYS* 1.3 78.5 - - - +
826A LEU* 1.3 68.9 + - - +
831A PRO* 4.2 0.2 - - - +
832A VAL* 2.9 37.3 + - + +
833A ALA* 3.0 21.4 + - + +
834A GLU* 5.9 0.7 - - - -
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Residues in contact with LEU 826 (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* 3.4 8.0 - - - +
781A THR* 2.8 45.8 + - + +
783A ILE* 3.3 33.4 - - + -
824A LYS* 4.9 11.4 - - + -
825A ILE* 1.3 82.4 - - - +
827A HIS* 1.3 60.5 + - - +
828A HIS 4.0 0.4 - - - -
829A TRP* 4.3 26.7 - - + +
830A VAL 3.3 7.9 - - - +
831A PRO* 3.8 24.0 - - + -
832A VAL* 4.0 4.5 - - - -
879A LEU* 4.1 19.3 - - + -
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Residues in contact with HIS 827 (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* 3.2 26.9 - - + +
779A THR* 3.0 27.4 + - - -
780A VAL* 4.7 5.4 - - + +
826A LEU* 1.3 74.0 - - - +
828A HIS* 1.3 97.8 + + - +
830A VAL* 2.8 32.0 + - + +
832A VAL* 3.7 17.9 - - + -
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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