Contacts of the helix formed by residues 717 - 726 (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 SER 717 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715D GLY 3.4 3.6 + - - -
716D ILE* 1.3 75.0 - - - +
718D ASP* 1.3 69.2 + - - +
719D TYR* 3.0 5.1 + - - +
720D GLY 3.1 7.8 + - - -
721D LEU* 3.0 20.4 + - - +
736D ILE* 3.8 4.7 - - - -
2F T 3.6 23.1 - - - -
3F 6OG 2.4 25.8 + - - -
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Residues in contact with ASP 718 (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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717D SER* 1.3 74.9 - - - +
719D TYR* 1.3 70.1 + - - +
721D LEU* 3.3 0.6 + - - -
722D ALA* 2.8 36.7 + - - +
729D ARG* 3.0 41.8 + - - +
732D ALA* 3.3 7.4 - - - +
733D ALA* 3.7 37.6 - - - +
736D ILE* 3.6 13.7 - - + +
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Residues in contact with TYR 719 (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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548D LYS* 5.6 6.1 - - - +
717D SER* 3.0 7.1 - - - +
718D ASP* 1.3 88.7 + - - +
720D GLY* 1.3 60.5 + - - +
722D ALA* 3.2 3.8 + - + +
723D GLN* 3.0 69.5 + - + +
729D ARG* 3.8 35.9 - - - +
2F T 3.4 62.7 - + + +
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Residues in contact with GLY 720 (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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716D ILE* 3.6 9.2 - - - -
717D SER 3.1 4.0 + - - -
719D TYR* 1.3 84.1 - - - +
721D LEU* 1.3 57.4 + - - +
723D GLN* 3.5 3.7 + - - +
724D ASN* 2.8 38.1 + - - +
3F 6OG 3.4 31.2 + - - -
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Residues in contact with LEU 721 (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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708D VAL* 4.1 22.7 - - + -
712D ILE* 4.2 16.2 - - + -
716D ILE* 3.5 18.6 - - + +
717D SER 3.0 14.9 + - - +
718D ASP* 3.6 4.7 - - - +
720D GLY* 1.3 77.6 - - - +
722D ALA* 1.3 55.6 + - - +
724D ASN* 3.9 3.3 - - + -
725D LEU* 2.9 54.7 + - + +
727D ILE* 5.2 1.6 - - + -
732D ALA* 3.5 32.3 - - + +
735D PHE* 4.3 11.0 - - + -
736D ILE* 3.8 17.0 - - + -
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Residues in contact with ALA 722 (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 20.0 + - - +
719D TYR* 3.2 5.1 + - + +
721D LEU* 1.3 71.3 - - - +
723D GLN* 1.3 62.2 + - - +
726D ASN* 2.6 34.1 + - - -
727D ILE* 3.1 29.7 + - - +
729D ARG* 4.0 22.7 - - + -
732D ALA* 4.0 5.8 - - + +
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Residues in contact with GLN 723 (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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548D LYS* 6.1 0.5 - - - +
559D ASP* 4.8 6.4 - - - +
563D LYS* 2.6 50.9 + - - +
719D TYR* 3.0 60.1 + - + +
720D GLY* 3.9 5.2 - - - +
722D ALA* 1.3 78.9 - - - +
724D ASN* 1.3 71.8 + - - +
726D ASN 3.6 0.5 + - - -
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Residues in contact with ASN 724 (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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559D ASP* 4.3 13.6 - - - +
704D GLN* 4.9 4.3 - - - +
707D ALA* 6.0 3.0 - - - +
708D VAL* 6.5 0.2 - - + -
716D ILE* 4.0 8.2 - - + +
720D GLY* 2.8 21.7 + - - +
721D LEU* 3.9 6.3 - - + +
723D GLN* 1.3 85.4 - - - +
725D LEU* 1.3 65.4 + - + +
726D ASN* 3.5 1.7 + - - +
3F 6OG 3.8 27.3 + - - -
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Residues in contact with LEU 725 (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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689D ILE* 3.7 35.7 - - + -
690D PHE* 5.7 1.6 - - + -
704D GLN* 4.0 22.7 - - + +
708D VAL* 3.7 25.6 - - + -
721D LEU* 2.9 38.9 + - + +
724D ASN* 1.3 77.7 - - + +
726D ASN* 1.3 73.0 + - - +
727D ILE* 3.4 32.4 - - + +
735D PHE* 5.9 5.2 - - + -
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Residues in contact with ASN 726 (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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562D GLU* 5.2 2.8 + - - +
563D LYS* 4.0 40.2 - - - +
722D ALA 2.6 18.8 + - - -
723D GLN 3.6 3.3 + - - +
724D ASN 3.3 4.1 - - - +
725D LEU* 1.3 78.5 - - - +
727D ILE* 1.3 58.7 + - - +
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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