Contacts of the helix formed by residues 828 - 836 (chain A) in PDB entry 1VDV
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 ASP 828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.1 20.5 - - - +
43A CYS 5.8 1.1 - - - +
269A LYS* 3.1 30.5 + - - -
270A PHE* 6.0 1.8 - - + -
606A ARG* 3.0 27.0 + - - -
679A GLU* 3.7 0.3 - - - +
746A THR* 4.4 0.2 - - - -
826A MET 3.7 3.7 + - - +
827A LEU* 1.3 77.3 - - - +
829A ARG* 1.3 68.4 + - - +
830A ASN* 3.4 18.5 - - - +
831A GLU* 2.9 13.9 + - - +
832A ASP* 3.0 19.1 + - - +
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Residues in contact with ARG 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 3.0 22.6 + - - +
43A CYS* 3.9 27.2 + - + +
45A GLU* 5.8 0.9 - - - +
740A ASP* 4.7 2.0 + - - -
742A PHE* 3.6 50.1 - - + +
743A TYR* 2.8 37.2 + - - +
744A LEU* 3.0 19.8 + - - +
746A THR* 3.6 24.5 - - - +
827A LEU 3.9 1.2 + - - -
828A ASP* 1.3 73.2 - - - +
830A ASN* 1.3 63.6 + - - +
832A ASP* 3.2 3.7 + - - +
833A MET* 2.9 45.2 + - - +
1222A ARG 4.7 0.7 - - - +
1223A GLY* 4.2 2.7 - - - -
1224A PRO* 4.2 13.7 - - + -
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Residues in contact with ASN 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE* 3.8 31.7 - - + +
606A ARG* 4.9 5.6 + - - +
828A ASP* 3.4 19.6 - - - +
829A ARG* 1.3 76.7 - - - +
831A GLU* 1.3 74.7 + - - +
833A MET 4.2 0.3 - - - -
834A LEU* 3.3 23.7 + - - +
1222A ARG* 3.2 37.0 + - + +
5005A GOL 3.4 14.4 + - - +
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Residues in contact with GLU 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A ARG* 3.0 55.4 + - - +
607A LEU* 4.4 13.7 + - - +
825A CYS* 5.7 1.4 - - - -
826A MET 4.5 1.6 - - - +
827A LEU* 3.6 24.7 - - + +
828A ASP* 2.9 29.1 + - + +
830A ASN* 1.3 89.3 + - - +
832A ASP* 1.3 58.3 + - - +
834A LEU* 3.3 5.0 + - - -
835A ILE* 2.9 49.1 + - + +
5019A GOL 4.4 4.9 + - - +
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Residues in contact with ASP 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A ASP* 5.0 3.1 - - - +
743A TYR* 2.6 33.7 + - - -
746A THR* 3.2 16.0 - - + -
747A HIS* 3.1 39.4 + - - -
827A LEU* 3.9 14.0 - - + +
828A ASP 3.0 12.2 + - - +
829A ARG* 3.2 12.1 + - - +
831A GLU* 1.3 77.7 - - - +
833A MET* 1.3 63.9 + - - +
836A THR* 2.7 35.0 + - - -
5304A CA 3.8 1.4 - - - -
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Residues in contact with MET 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A ASP* 3.2 38.0 - - + +
742A PHE* 4.4 3.1 - - - -
829A ARG* 2.9 31.5 + - - +
830A ASN 4.2 2.9 - - - +
832A ASP* 1.3 78.4 - - + +
834A LEU* 1.3 60.9 + - - +
837A GLY* 5.0 7.3 + - - +
1211A LEU* 4.0 5.3 - - + +
1219A LEU* 3.5 14.5 - - + +
1221A THR 3.6 14.1 - - - +
1222A ARG* 3.4 11.4 - - - +
1223A GLY* 3.3 30.5 - - - +
1227A TYR* 3.5 43.1 - - + -
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Residues in contact with LEU 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A THR* 4.5 8.5 - - - +
610A SER 5.4 0.2 - - - +
663A VAL* 3.8 23.3 - - + +
664A GLY* 3.9 22.9 - - - +
830A ASN 3.3 16.2 + - - +
831A GLU* 3.3 4.9 + - - +
832A ASP 3.2 0.6 - - - -
833A MET* 1.3 82.9 - - - +
835A ILE* 1.3 58.3 + - + +
837A GLY 4.9 0.7 + - - -
906A SER* 2.7 30.3 + - - -
1219A LEU* 4.0 18.5 - - + +
1222A ARG* 3.7 44.9 - - - +
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Residues in contact with ILE 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A LEU* 4.2 19.1 - - + -
609A THR* 3.6 25.6 - - + +
664A GLY* 3.7 12.6 - - - +
666A ILE* 4.2 8.7 - - + -
804A ARG* 5.1 0.2 + - - -
807A LEU* 3.9 13.8 - - + +
827A LEU* 5.2 3.1 - - + -
831A GLU* 2.9 34.0 + - + +
834A LEU* 1.3 87.8 - - + +
836A THR* 1.3 67.7 + - + +
837A GLY 3.4 4.1 + - - -
906A SER* 3.7 5.5 - - - -
907A SER 5.1 0.2 + - - -
5018A GOL 3.4 44.1 - - - -
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Residues in contact with THR 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A HIS* 3.4 36.1 - - + +
800A GLY 5.0 0.6 - - - +
804A ARG* 3.2 36.0 - - - +
807A LEU* 4.4 8.7 - - + -
808A VAL* 5.7 1.8 - - + -
827A LEU* 3.9 18.8 - - + -
832A ASP* 2.7 25.8 + - - +
835A ILE* 1.3 78.8 - - + +
837A GLY* 1.3 60.1 + - - +
907A SER 4.4 1.8 - - - -
909A THR* 4.1 1.7 - - - +
5304A CA 2.5 25.1 - - - -
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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