Contacts of the strand formed by residues 822 - 830 (chain A) in PDB entry 2I6W
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 LEU 822 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685A ILE* 3.3 22.4 - - + -
686A ASP 4.3 12.8 - - - +
687A GLN* 3.0 40.4 - - + +
818A ARG* 3.0 3.1 - - - +
819A TYR 2.8 33.0 + - - +
820A ASN* 3.2 11.1 - - + +
821A GLY* 1.3 77.8 - - - +
823A PRO* 1.3 72.3 - - + +
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Residues in contact with PRO 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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58A GLN* 5.0 2.2 - - - +
685A ILE* 3.6 1.9 - - - -
686A ASP* 3.1 58.4 + - + +
690A LEU 5.3 0.4 - - - +
691A GLY* 6.0 1.1 - - - -
695A LEU* 3.5 14.6 - - + -
817A GLU 3.4 4.7 - - - +
818A ARG* 3.4 33.1 - - - +
822A LEU* 1.3 91.1 - - + +
824A SER* 1.3 58.8 + - - +
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Residues in contact with SER 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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683A GLU* 3.0 27.2 - - - +
684A LEU 2.3 28.1 + - - -
685A ILE* 3.8 2.3 + - - -
695A LEU* 4.3 5.6 - - - +
721A LEU* 5.3 0.2 - - - +
817A GLU* 3.0 29.3 + - - +
818A ARG 3.8 3.8 - - - -
819A TYR* 3.5 28.4 - - - +
822A LEU 3.5 0.2 + - - -
823A PRO* 1.3 75.6 - - - +
825A MET* 1.3 70.5 + - - +
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Residues in contact with MET 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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682A PHE 3.7 0.2 - - - +
683A GLU* 3.4 3.1 - - - -
684A LEU* 3.0 37.8 + - + +
692A HIS* 4.9 2.7 - - + -
695A LEU* 4.0 12.6 - - + +
696A THR* 3.1 40.4 - - + -
699A ARG* 3.0 46.4 - - + +
718A PRO* 5.2 3.4 - - + -
721A LEU* 3.0 38.8 - - + -
817A GLU* 3.9 5.4 - - - +
824A SER* 1.3 87.6 - - - +
826A GLU* 1.3 63.4 + - - +
827A ILE* 3.7 4.8 + - - +
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Residues in contact with GLU 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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681A ASP* 2.6 38.1 - - - +
682A PHE 3.3 2.9 - - - +
683A GLU* 3.1 22.6 + - - +
718A PRO* 3.3 6.8 - - - +
719A ASN* 3.1 53.6 + - + +
817A GLU* 3.5 15.6 + - - +
825A MET* 1.3 71.7 - - - +
827A ILE* 1.3 63.3 + - - +
828A LEU* 3.9 9.4 - - + +
860A THR* 5.2 1.0 + - - +
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Residues in contact with ILE 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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680A PHE* 4.4 8.1 - - + -
681A ASP* 3.5 1.0 - - - -
682A PHE* 2.5 63.2 + - + +
684A LEU* 5.3 4.5 - - + -
699A ARG* 4.2 25.1 - - + -
702A LEU* 3.7 30.7 - - + -
703A LEU* 4.0 24.0 - - + -
716A VAL* 5.0 2.5 - - + -
717A ARG 3.3 11.9 - - - +
718A PRO* 4.8 2.2 - - + -
825A MET 4.5 6.1 - - - +
826A GLU* 1.3 76.7 - - - +
828A LEU* 1.3 74.1 + - - +
844A MET* 5.0 4.9 - - - -
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Residues in contact with LEU 828 (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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680A PHE* 3.9 15.7 - - - +
681A ASP* 3.7 29.4 - - - +
716A VAL* 3.6 2.8 - - - -
717A ARG* 3.0 57.3 + - + +
718A PRO 4.9 2.2 - - - +
719A ASN* 3.9 30.5 - - - +
826A GLU* 3.9 12.7 - - + +
827A ILE* 1.3 84.1 - - - +
829A GLY* 1.3 60.5 + - - +
862A MET* 4.5 8.5 - - + -
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Residues in contact with GLY 829 (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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678A THR 4.0 0.3 - - - +
679A GLY* 3.7 0.2 - - - -
680A PHE* 3.2 43.1 + - - +
714A THR 4.1 0.2 - - - -
715A SER 3.5 8.3 - - - -
716A VAL* 4.4 0.2 - - - -
717A ARG* 3.0 15.4 - - - +
828A LEU* 1.3 80.0 - - - +
830A GLN* 1.3 72.6 + - - -
862A MET* 4.9 0.9 - - - +
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Residues in contact with GLN 830 (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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678A THR* 2.9 45.0 + - - +
679A GLY* 4.4 0.7 + - - -
680A PHE* 3.6 12.3 - - - -
713A LEU* 4.5 0.7 - - - -
714A THR* 2.8 36.0 + - - +
715A SER* 4.2 11.9 - - - +
717A ARG* 4.1 14.3 - - - +
829A GLY* 1.3 88.6 + - - +
831A ALA* 1.3 73.3 + - - +
832A ALA* 4.8 0.9 - - - +
862A MET* 5.6 0.8 - - - +
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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