Contacts of the helix formed by residues 1694 - 1702 (chain D) in PDB entry 3DQV
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 LEU1694 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1539D SER* 4.5 12.8 - - - +
1541D GLU* 4.8 8.5 - - + +
1543D VAL* 3.9 34.8 - - + -
1574D HIS* 6.0 2.9 - - + -
1576D LEU* 3.6 20.2 - - + -
1598D PHE* 4.6 4.5 - - + -
1629D GLU* 3.3 36.3 - - + +
1632D ARG* 4.2 0.4 - - - +
1693D GLN* 1.3 77.9 - - + +
1695D THR* 1.3 60.7 + - - +
1696D THR* 4.1 9.4 - - - +
1697D GLU* 2.9 28.3 + - + +
1698D ARG* 2.8 25.1 + - - +
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Residues in contact with THR1695 (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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1628D ALA* 4.8 13.0 + - + +
1629D GLU* 3.0 12.0 + - - -
1632D ARG* 3.7 32.2 + - + +
1693D GLN 3.8 2.0 + - - -
1694D LEU* 1.3 67.7 - - - +
1696D THR* 1.3 66.1 + - - +
1698D ARG* 4.0 9.9 - - + -
1699D MSE 3.0 52.5 + - + +
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Residues in contact with THR1696 (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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1541D GLU* 3.5 28.1 + - - +
1628D ALA* 4.6 10.9 - - - +
1629D GLU* 3.8 8.7 + - - +
1694D LEU* 3.0 7.7 - - - +
1695D THR* 1.3 81.2 - - - +
1697D GLU* 1.3 64.9 + - - +
1699D MSE 3.7 10.8 + - - +
1700D ARG* 2.8 32.0 + - + +
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Residues in contact with GLU1697 (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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1538D ARG 3.9 19.5 - - - +
1539D SER* 2.9 27.4 + - - -
1541D GLU* 3.5 23.6 - - - +
1693D GLN* 3.9 22.0 - - + +
1694D LEU* 2.9 19.0 + - + +
1696D THR* 1.3 81.0 - - - +
1698D ARG* 1.3 60.7 + - - +
1700D ARG* 3.0 18.8 + - - +
1701D GLU* 2.7 34.1 - - - +
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Residues in contact with ARG1698 (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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1406D GLU* 4.2 1.0 + - - -
1452D ARG* 2.7 29.8 + - - +
1453D TYR* 2.6 42.8 + - - +
1456D ALA* 5.7 6.9 - - - +
1693D GLN* 3.3 23.5 + - - +
1694D LEU 2.8 16.7 + - - +
1695D THR* 3.3 14.1 + - + +
1697D GLU* 1.3 72.5 - - - +
1699D MSE 1.3 62.0 + - + +
1700D ARG 2.8 6.6 + - - -
1701D GLU* 3.5 3.0 + - - +
1702D GLU* 3.0 37.3 + - - +
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Residues in contact with MSE1699 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1658D LYS* 5.4 15.0 - - - -
1695D THR* 3.0 42.9 + - + +
1696D THR* 4.3 7.4 - - - +
1698D ARG* 1.3 71.3 - - + +
1700D ARG* 1.3 63.4 + - - +
1702D GLU* 3.8 24.5 - - - +
1703D GLU* 3.3 20.6 + - - +
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Residues in contact with ARG1700 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1696D THR* 2.8 34.1 - - + +
1697D GLU* 3.0 20.3 + - - +
1698D ARG 2.8 2.6 + - - -
1699D MSE 1.3 75.6 - - - +
1701D GLU* 1.3 73.1 + - - +
1702D GLU 3.1 0.7 - - - -
1703D GLU* 3.1 24.5 + - - +
1704D ASN* 3.4 10.4 + - - -
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Residues in contact with GLU1701 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1452D ARG* 3.6 28.7 + - - +
1538D ARG 5.5 1.2 - - - +
1693D GLN* 4.7 8.5 + - - -
1697D GLU* 2.7 36.9 - - - +
1698D ARG* 3.9 3.1 - - - +
1700D ARG* 1.3 75.8 - - - +
1702D GLU* 1.3 57.4 + - - +
1703D GLU 3.0 2.2 - - - -
1704D ASN* 2.8 13.6 + - + +
1705D GLU* 2.7 41.6 + - + +
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Residues in contact with GLU1702 (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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1452D ARG* 4.3 3.7 - - - +
1698D ARG* 3.0 32.9 + - + +
1699D MSE 3.8 27.3 + - - +
1701D GLU* 1.3 80.1 - - - +
1703D GLU* 1.3 57.9 + - - +
1704D ASN 3.7 0.2 + - - -
1705D GLU* 4.2 16.1 + - - +
1706D GLY* 4.1 10.2 + - - -
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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