Contacts of the strand formed by residues 831 - 837 (chain D) in PDB entry 2HHW
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 831 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637D ARG* 5.0 10.6 + - - -
651D ALA* 5.3 2.5 - - + +
652D ALA 3.1 10.1 - - - +
653D ASP* 3.6 31.4 - - + +
804D ILE* 3.4 1.5 - - - +
827D GLN* 3.3 4.5 - - - -
828D VAL* 2.8 43.8 + - + +
830D ASP* 1.3 87.0 - - - +
832D LEU* 1.3 67.5 + - - +
833D ILE* 4.0 19.9 - - + +
852D MET* 5.1 0.2 - - - -
872D TRP* 5.3 0.9 + - - -
880D D3T 5.5 0.2 + - - -
29E DDG 3.6 32.6 + - - +
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Residues in contact with LEU 832 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650D PHE 3.9 0.9 - - - +
651D ALA* 3.5 2.8 - - - -
652D ALA 2.9 32.1 + - - +
804D ILE* 3.7 19.1 - - + -
807D ALA* 4.7 1.3 - - + -
808D MET* 3.5 40.8 - - + +
811D LEU* 4.0 22.2 - - + -
824D LEU* 4.0 13.9 - - + -
826D LEU 3.6 3.1 - - - +
827D GLN* 3.8 13.0 - - + -
831D GLU* 1.3 83.1 - - - +
833D ILE* 1.3 62.2 + - - +
834D LEU* 4.0 9.1 - - + +
852D MET* 4.1 30.3 - - + -
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Residues in contact with ILE 833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D ILE* 3.8 26.9 - - + -
650D PHE 3.4 2.9 - - - +
651D ALA* 3.3 27.6 - - + -
824D LEU* 3.8 2.8 - - - +
825D LEU* 2.8 32.3 + - + -
826D LEU* 2.8 37.0 + - + +
828D VAL* 4.5 8.3 - - + -
831D GLU* 4.0 18.4 - - + +
832D LEU* 1.3 76.5 - - - +
834D LEU* 1.3 66.0 + - - +
872D TRP* 3.8 31.9 - - + +
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Residues in contact with LEU 834 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D ILE* 3.4 9.2 - - - +
650D PHE* 2.8 53.2 + - + +
811D LEU* 4.0 15.7 - - + -
815D LEU* 4.0 26.5 - - + -
822D ALA* 4.8 0.9 - - + -
823D HIS 3.2 21.3 - - - +
824D LEU* 3.8 16.6 - - + +
825D LEU* 4.0 6.4 - - - +
832D LEU* 4.0 17.7 - - + +
833D ILE* 1.3 79.2 - - - +
835D GLU* 1.3 65.4 + - - +
844D LEU* 4.8 11.0 - - + -
848D VAL* 4.6 17.0 - - + -
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Residues in contact with GLU 835 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491D ALA* 5.7 0.5 - - - +
492D GLY 5.0 0.7 - - - +
493D VAL* 6.1 0.2 - - - -
494D LYS 5.8 0.7 + - - -
601D LYS* 5.7 0.2 + - - -
641D VAL 4.5 1.0 - - - +
642D PRO* 3.4 6.8 - - + +
643D SER* 2.6 50.4 + - - -
647D TRP* 3.7 11.8 - - + -
648D LEU 3.1 11.7 - - - +
649D ILE* 4.1 5.6 - - + -
650D PHE* 5.9 0.2 - - - -
822D ALA* 3.4 1.6 - - - +
823D HIS* 2.7 55.6 + - + +
825D LEU* 3.5 26.4 - - + +
834D LEU* 1.3 76.5 - - - +
836D ALA* 1.3 65.3 + - - +
844D LEU* 5.5 0.4 - - - -
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Residues in contact with ALA 836 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647D TRP* 3.1 11.4 - - - -
648D LEU* 2.8 33.1 + - - +
822D ALA* 3.3 24.9 - - + +
835D GLU* 1.3 78.4 - - - +
837D PRO* 1.3 76.5 - - + +
840D GLU* 4.0 4.5 - - + +
841D MET* 4.7 3.7 - - + +
844D LEU* 3.8 18.8 - - + -
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Residues in contact with PRO 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D ASP 4.6 0.2 - - - +
647D TRP* 3.4 43.1 - - + +
821D GLN* 3.6 26.9 - - + +
822D ALA 4.2 0.2 - - - +
836D ALA* 1.3 92.3 - - + +
838D LYS* 1.3 67.7 - - - +
839D GLU* 3.7 15.7 - - + +
840D GLU* 2.9 39.0 + - + +
841D MET* 3.6 5.2 + - - +
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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