Contacts of the helix formed by residues 718 - 727 (chain D) in PDB entry 5TWV
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 GLY 718 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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688D TRP* 5.7 2.7 - - - -
716D GLY 3.1 6.5 - - - +
717D CYS* 1.3 78.5 - - - +
719D LYS* 1.3 55.3 + - - +
720D SER 3.4 2.5 - - - -
721D SER* 3.2 17.5 + - - -
722D LEU* 2.5 36.9 + - - +
906D GLY* 5.0 6.7 - - - -
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Residues in contact with LYS 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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711D ILE* 5.5 10.8 - - + +
712D VAL* 5.5 8.1 - - - +
713D GLY* 5.4 8.5 - - - +
714D GLN 5.4 4.3 - - - +
717D CYS* 3.7 3.7 - - + +
718D GLY* 1.3 76.7 - - - +
720D SER* 1.3 57.7 + - - +
722D LEU* 3.2 9.9 + - - +
723D LEU* 2.9 26.0 + - - +
887D VAL* 5.4 11.3 - - + +
903D MET* 6.3 3.1 - - + -
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Residues in contact with SER 720 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688D TRP* 5.3 4.7 - - - -
718D GLY 3.4 0.4 - - - -
719D LYS* 1.3 77.6 - - - +
721D SER* 1.3 57.3 + - - +
723D LEU* 3.2 10.5 + - - +
724D LEU* 2.9 25.0 + - - +
772D TYR* 5.7 0.5 + - - -
775D GLN* 4.1 25.8 - - - -
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Residues in contact with SER 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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686D PHE* 5.3 4.4 - - - +
688D TRP* 3.5 40.7 - - - -
695D THR* 5.9 3.6 - - - -
696D LEU* 6.4 2.0 - - - -
718D GLY* 3.2 18.0 + - - -
720D SER* 1.3 75.9 - - - +
722D LEU* 1.3 59.1 + - - +
724D LEU* 3.2 11.1 + - - +
725D ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 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 GLY 2.5 20.3 + - - +
719D LYS* 3.2 11.2 + - - +
721D SER* 1.3 72.1 - - - +
723D LEU* 1.3 57.8 + - - +
725D ALA* 3.2 10.0 + - - +
726D THR* 2.9 26.7 + - - -
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Residues in contact with LEU 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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719D LYS 2.9 13.7 + - - +
720D SER* 3.2 13.4 + - - +
722D LEU* 1.3 74.8 - - - +
724D LEU* 1.3 58.0 + - - +
726D THR* 3.2 11.0 + - - -
727D LEU* 2.9 27.4 + - - +
772D TYR* 5.3 17.0 - - + +
852D PHE* 5.7 7.4 - - + -
854D ASP* 5.4 10.5 - - + -
887D VAL* 5.6 8.7 - - + -
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Residues in contact with LEU 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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688D TRP* 5.8 5.2 - - + -
720D SER 2.9 13.5 + - - +
721D SER* 3.2 13.7 + - - +
723D LEU* 1.3 73.2 - - - +
725D ALA* 1.3 62.5 + - - +
727D LEU* 3.1 11.3 + - - +
729D GLU* 2.8 43.9 + - + +
730D MET* 4.7 3.4 - - + +
772D TYR* 5.5 4.4 + - - +
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Residues in contact with ALA 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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686D PHE* 4.1 22.9 - - + -
696D LEU* 6.0 0.9 - - + -
721D SER 2.9 13.1 + - - +
722D LEU* 3.3 12.8 - - - +
724D LEU* 1.3 75.0 - - - +
726D THR* 1.3 62.8 + - - +
728D GLY* 3.1 13.2 + - - +
729D GLU 4.8 0.4 - - - +
730D MET* 4.7 10.4 - - + +
739D TRP* 4.8 10.6 - - - -
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Residues in contact with THR 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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722D LEU 2.9 14.2 + - - -
723D LEU* 3.2 13.4 + - - -
725D ALA* 1.3 75.3 - - - +
727D LEU* 1.3 58.4 + - - +
728D GLY 3.3 0.6 + - - -
739D TRP* 5.6 10.3 - - - -
852D PHE* 6.0 6.1 - - - -
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Residues in contact with LEU 727 (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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723D LEU 2.9 15.2 + - - +
724D LEU* 3.6 9.2 - - - +
725D ALA 3.1 0.8 - - - -
726D THR* 1.3 76.3 - - - +
728D GLY* 1.3 61.6 + - - +
729D GLU* 3.3 7.5 + - + +
772D TYR* 5.3 17.9 - - + -
1215D ARG* 5.6 8.2 - - + +
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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