Contacts of the strand formed by residues 647 - 654 (chain D) in PDB entry 2HVH
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 TRP 647 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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642D PRO* 3.2 24.3 - - + +
643D SER* 4.9 3.6 - - - -
644D GLU* 3.4 42.7 + - + +
645D SER 3.1 17.3 + - - -
646D ASP* 1.3 85.2 + - - +
648D LEU* 1.3 71.4 + - - +
821D GLN* 3.7 39.6 - - + +
823D HIS* 3.9 22.4 - + - -
835D GLU* 3.8 22.2 - - + -
836D ALA* 3.3 29.8 - - - +
837D PRO* 3.5 27.5 - - + +
838D LYS* 4.9 0.5 - - - -
870D SER* 5.4 0.2 - - - -
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Residues in contact with LEU 648 (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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642D PRO* 3.8 7.4 - - - -
647D TRP* 1.3 83.3 - - - +
649D ILE* 1.3 65.0 + - - +
650D PHE 4.0 0.2 + - - -
835D GLU* 3.3 5.9 - - - +
836D ALA 2.8 30.7 + - - +
838D LYS* 3.9 37.0 - - + +
841D MET* 3.8 34.7 - - + +
868D TYR* 4.3 16.4 - - + -
869D GLY* 3.6 22.9 - - - +
870D SER* 3.8 16.4 - - - +
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Residues in contact with ILE 649 (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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493D VAL* 5.8 1.6 - - + -
640D PHE* 4.5 2.0 - - + +
641D VAL 4.3 4.7 - - - +
642D PRO* 3.9 29.1 - - + +
648D LEU* 1.3 73.7 - - - +
650D PHE* 1.3 62.1 + - - +
651D ALA* 5.4 0.2 - - + -
825D LEU* 3.7 29.2 - - + -
833D ILE* 4.1 18.4 - - + -
834D LEU 3.5 7.2 - - - +
835D GLU* 3.9 8.7 - - + -
841D MET* 5.3 0.2 - - - -
868D TYR* 3.2 6.6 - - - +
869D GLY 2.9 37.6 + - - +
871D THR 4.1 4.7 - - - +
872D TRP* 4.0 25.1 - - + +
875D ALA* 3.8 18.4 - - + -
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Residues in contact with PHE 650 (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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648D LEU 4.0 0.2 + - - -
649D ILE* 1.3 76.9 - - - +
651D ALA* 1.3 66.7 + - - +
652D ALA* 3.8 14.4 - - + -
832D LEU 3.7 0.2 - - - +
833D ILE* 3.5 4.9 - - - +
834D LEU* 2.8 56.9 + - + +
835D GLU* 5.6 0.2 - - - -
841D MET* 4.0 25.8 - - + -
844D LEU* 3.8 42.6 - - + -
845D CYS* 4.1 16.6 - - - -
848D VAL* 3.8 26.0 - - + -
849D PRO* 4.7 0.9 - - + -
866D TYR* 3.6 25.6 - + + -
867D HIS 3.7 5.4 - - - -
868D TYR* 4.1 7.9 - + + -
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Residues in contact with ALA 651 (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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650D PHE* 1.3 77.5 - - - +
652D ALA* 1.3 60.3 + - - +
653D ASP* 5.9 0.4 - - - -
831D GLU* 4.9 4.5 - - - +
832D LEU 3.5 4.0 - - - -
833D ILE* 3.8 21.5 - - + -
865D ASP 4.5 0.2 - - - -
866D TYR* 3.1 6.4 - - - +
867D HIS* 2.8 35.7 + - - +
872D TRP* 5.1 2.9 - - - +
875D ALA* 4.2 9.8 - - + +
876D LYS 3.8 22.7 - - - +
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Residues in contact with ALA 652 (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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650D PHE* 3.8 16.8 - - + -
651D ALA* 1.3 75.3 - - - +
653D ASP* 1.3 59.8 + - - +
831D GLU* 3.2 4.0 - - - -
832D LEU 2.8 38.1 + - - +
833D ILE* 5.1 0.4 - - - +
848D VAL* 3.9 6.7 - - + -
849D PRO 5.6 0.2 - - - -
852D MET* 3.6 23.5 - - - +
864D VAL* 3.8 18.2 - - + -
865D ASP 3.2 5.8 - - - +
866D TYR* 4.1 2.2 - - + -
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Residues in contact with ASP 653 (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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651D ALA 5.9 0.2 - - - -
652D ALA* 1.3 73.2 - - - +
654D TYR* 1.3 63.1 + - - +
655D SER 3.4 0.7 + - - -
830D ASP* 3.0 8.7 - - - +
831D GLU* 3.8 26.0 - - + +
864D VAL* 4.0 4.4 - - - +
865D ASP* 2.8 45.2 + - + +
878D MN 2.3 35.1 + - - -
881D DCT 3.7 11.8 + - - -
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Residues in contact with TYR 654 (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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652D ALA 4.4 0.2 - - - -
653D ASP* 1.3 74.3 + - - +
655D SER* 1.3 57.6 + - - +
657D ILE* 3.8 33.4 + - + -
803D ILE* 4.0 10.6 - - + +
804D ILE* 4.2 28.3 - - + -
807D ALA* 3.5 12.9 - - + +
830D ASP* 3.1 27.6 + - + +
852D MET* 2.5 55.1 + - + +
855D ALA* 4.0 5.2 - - - +
862D LEU* 4.2 20.4 - - + -
863D LYS 3.5 7.4 - - - -
864D VAL* 3.5 20.4 - - + +
878D MN 2.3 36.2 + - - -
881D DCT 3.1 2.8 + - - -
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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