Contacts of the helix formed by residues 728 - 743 (chain D) in PDB entry 2HVI
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 SER 728 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727D ILE* 1.3 77.3 - - - +
729D ARG* 1.3 64.4 + - - +
730D LYS* 3.4 9.3 + - - +
731D GLU* 2.8 44.7 + - - +
732D ALA 3.0 16.5 + - - -
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Residues in contact with ARG 729 (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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718D ASP* 2.8 46.0 + - + +
719D TYR* 3.6 36.9 - - - +
722D ALA* 3.8 13.8 - - + +
727D ILE 3.5 2.0 + - - -
728D SER* 1.3 73.2 - - - +
730D LYS* 1.3 58.0 + - - +
732D ALA* 3.4 1.4 + - - +
733D ALA* 3.0 27.7 + - - +
1F A 4.9 5.3 - - - +
2F T 3.4 31.5 + - - +
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Residues in contact with LYS 730 (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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728D SER* 3.0 9.1 + - - +
729D ARG* 1.3 76.9 - - - +
731D GLU* 1.3 72.6 + - + +
733D ALA* 3.3 5.9 + - - +
734D GLU* 2.7 59.9 + - + +
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Residues in contact with GLU 731 (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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727D ILE* 3.6 20.2 - - + +
728D SER* 2.8 52.1 + - - +
730D LYS* 1.3 84.2 - - - +
732D ALA* 1.3 57.7 + - - +
734D GLU* 3.3 9.5 + - - +
735D PHE* 2.8 30.3 + - - +
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Residues in contact with ALA 732 (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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718D ASP* 3.3 28.9 - - - +
721D LEU* 3.7 9.4 - - + +
722D ALA* 3.7 16.2 - - + +
727D ILE* 3.6 13.2 - - + +
728D SER 3.0 12.0 + - - +
729D ARG 3.5 6.5 - - - +
730D LYS 3.2 0.2 - - - -
731D GLU* 1.3 78.4 - - - +
733D ALA* 1.3 62.2 + - - +
735D PHE* 3.2 3.4 + - - +
736D ILE* 3.1 28.7 + - - +
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Residues in contact with ALA 733 (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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718D ASP* 3.8 21.2 - - + +
729D ARG 3.0 17.3 + - - +
730D LYS* 3.7 5.8 - - - +
732D ALA* 1.3 75.8 - - - +
734D GLU* 1.3 59.4 + - + +
736D ILE* 3.3 7.3 + - - +
737D GLU* 3.0 28.7 + - - +
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Residues in contact with GLU 734 (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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730D LYS* 2.7 58.7 + - + +
731D GLU* 3.6 7.6 - - - +
733D ALA* 1.3 78.5 - - + +
735D PHE* 1.3 57.5 + - - +
737D GLU* 3.3 11.2 + - - +
738D ARG* 2.9 37.5 + - + +
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Residues in contact with PHE 735 (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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685D THR* 4.4 10.1 - - + -
688D ASP* 3.7 27.4 - - + -
689D ILE* 3.3 38.1 - - + -
708D VAL* 3.8 7.9 - - + -
712D ILE* 3.6 29.4 - - + -
721D LEU* 3.9 12.6 - - + -
725D LEU* 5.6 0.9 - - + -
727D ILE* 5.5 3.4 - - + -
731D GLU 2.8 17.1 + - - +
732D ALA* 3.6 6.3 - - - +
734D GLU* 1.3 76.4 - - - +
736D ILE* 1.3 56.4 + - - +
738D ARG* 3.2 26.7 + - + +
739D TYR* 2.8 40.7 + + - +
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Residues in contact with ILE 736 (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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712D ILE* 4.3 12.8 - - + -
716D ILE* 3.8 25.6 - - + +
717D SER* 3.9 4.9 - - - +
718D ASP* 3.9 25.4 - - + +
721D LEU* 3.7 16.2 - - + -
732D ALA 3.1 16.8 + - - +
733D ALA* 3.6 7.4 - - - +
735D PHE* 1.3 75.0 - - - +
737D GLU* 1.3 64.3 + - - +
739D TYR* 3.1 8.8 + - - +
740D PHE* 3.0 49.4 + - + -
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Residues in contact with GLU 737 (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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733D ALA 3.0 17.4 + - - +
734D GLU* 3.5 12.0 - - - +
735D PHE 3.2 0.2 - - - -
736D ILE* 1.3 77.8 - - - +
738D ARG* 1.3 63.2 + - + +
740D PHE* 3.4 6.0 + - - +
741D GLU* 3.1 45.8 + - + +
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Residues in contact with ARG 738 (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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688D ASP* 2.7 33.1 + - - -
734D GLU* 2.9 21.8 + - + +
735D PHE* 3.5 36.6 - - + +
737D GLU* 1.3 75.7 - - + +
739D TYR* 1.3 64.7 - - - +
741D GLU* 3.1 30.0 + - - +
742D SER* 3.2 16.3 + - - -
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Residues in contact with TYR 739 (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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659D LEU* 5.2 3.1 - - - +
671D LEU* 5.9 1.2 - - - +
681D ILE* 4.5 5.1 - - + +
685D THR* 4.4 7.2 - - + -
709D ASN* 2.8 43.9 + - - +
712D ILE* 3.5 35.0 - - + -
713D VAL* 3.9 24.2 - - + +
735D PHE* 2.8 28.8 + + - +
736D ILE* 3.1 14.1 + - - +
738D ARG* 1.3 76.3 - - - +
740D PHE* 1.3 65.0 + + - +
742D SER* 3.1 10.5 + - - -
743D PHE* 3.0 58.2 + + + -
746D VAL* 6.2 0.4 - - + -
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Residues in contact with PHE 740 (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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712D ILE* 3.6 33.7 - - + -
713D VAL* 4.7 3.6 - - - -
736D ILE* 3.0 46.1 + - + +
737D GLU* 4.1 4.9 - - - +
739D TYR* 1.3 81.6 - + - +
741D GLU* 1.3 61.0 + - - +
742D SER 3.2 0.2 - - - -
743D PHE* 3.3 6.9 - - + +
744D PRO* 3.1 29.5 - - - +
746D VAL* 4.2 21.8 - - + -
747D LYS* 3.7 47.4 - - + +
750D MET* 5.5 4.5 - - + -
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Residues in contact with GLU 741 (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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670D ASN* 5.0 1.7 + - - -
737D GLU* 3.1 45.2 + - + +
738D ARG* 3.1 24.1 + - - +
740D PHE* 1.3 79.1 - - - +
742D SER* 1.3 60.7 + - - +
744D PRO* 3.5 11.8 - - - +
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Residues in contact with SER 742 (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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670D ASN* 2.7 31.4 + - - +
738D ARG 3.2 10.1 + - - -
739D TYR* 3.1 11.9 + - - -
741D GLU* 1.3 79.9 - - - +
743D PHE* 1.3 81.2 + - - +
744D PRO* 3.4 2.3 - - - +
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Residues in contact with PHE 743 (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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668D ASP* 2.9 30.1 - - - +
670D ASN* 4.0 7.9 - - + -
671D LEU* 3.7 39.0 - - + -
674D ALA* 5.5 0.9 - - + -
681D ILE* 4.9 14.4 - - + -
739D TYR* 3.0 61.2 + + + +
740D PHE* 3.3 10.8 - - + +
741D GLU 3.3 0.2 - - - -
742D SER* 1.3 99.9 - - - +
744D PRO* 1.3 61.7 - - - +
746D VAL* 3.1 23.8 + - + +
747D LYS 3.3 8.1 + - - -
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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