Contacts of the helix formed by residues 1514 - 1523 (chain H) in PDB entry 2VKZ
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 ASN1514 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967B VAL* 3.6 3.5 - - - +
1428H GLU* 4.7 0.4 + - - -
1470H THR* 3.5 30.4 + - - +
1480H PHE* 5.3 0.8 - - - -
1483H VAL* 4.3 13.0 - - + -
1485H CYS* 3.5 8.0 - - - +
1506H TYR* 4.3 2.8 - - - -
1513H GLY* 1.3 71.3 - - - -
1515H PRO* 1.3 67.1 - - - +
1516H VAL* 3.1 21.8 + - - +
1517H VAL* 3.3 33.0 + - + +
1518H ASP* 3.2 21.3 + - - +
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Residues in contact with PRO1515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964B GLU* 3.5 32.0 - - + +
967B VAL* 3.5 14.8 - - + -
968B VAL* 3.3 17.9 - - + -
1447H LYS* 5.3 1.0 + - - -
1449H TRP* 5.2 3.1 - - - +
1506H TYR* 3.1 40.6 - - + +
1513H GLY 3.2 8.7 - - - +
1514H ASN* 1.3 90.0 - - - +
1516H VAL* 1.3 59.5 + - + +
1518H ASP* 3.3 4.9 + - + +
1519H PHE* 2.9 30.5 + - - +
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Residues in contact with VAL1516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1449H TRP* 3.7 43.0 - - + +
1468H THR* 4.8 2.2 - - + +
1485H CYS* 4.1 13.0 - - + -
1504H VAL* 3.8 21.8 - - + -
1506H TYR* 3.6 35.4 - - + -
1514H ASN* 3.1 8.4 + - - +
1515H PRO* 1.3 77.0 - - - +
1517H VAL* 1.3 58.7 + - + +
1519H PHE* 3.5 2.3 + - - +
1520H LEU* 3.0 39.6 + - + +
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Residues in contact with VAL1517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428H GLU* 3.5 37.0 - - + +
1431H TYR* 3.6 16.4 - - + +
1468H THR* 4.5 8.1 - - + -
1470H THR* 4.5 0.2 - - + -
1485H CYS* 4.5 0.4 - - - -
1514H ASN* 3.3 33.2 + - + +
1515H PRO 3.4 0.2 - - - -
1516H VAL* 1.3 78.6 - - + +
1518H ASP* 1.3 61.3 + - - +
1520H LEU* 3.4 6.2 + - + +
1521H LYS* 2.8 55.2 + - - +
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Residues in contact with ASP1518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963B LEU* 5.0 7.6 - - - +
964B GLU* 5.9 0.3 - - - -
967B VAL* 3.9 26.7 - - + +
1514H ASN 3.2 17.0 + - - +
1515H PRO* 3.6 4.9 - - - +
1517H VAL* 1.3 79.3 - - - +
1519H PHE* 1.3 64.2 + - - +
1521H LYS* 3.3 13.3 + - - +
1522H ARG* 3.1 58.6 + - - +
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Residues in contact with PHE1519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960B GLU* 3.2 30.1 - - + -
1433H MET* 3.8 21.8 - - + -
1443H VAL* 3.8 26.0 - - + -
1444H LEU* 3.8 24.2 - - + -
1447H LYS* 4.1 19.7 - - + +
1449H TRP* 3.9 16.8 - + + -
1515H PRO 2.9 17.4 + - - +
1516H VAL 3.5 4.9 - - - +
1518H ASP* 1.3 78.2 + - - +
1520H LEU* 1.3 70.9 + - + +
1522H ARG* 3.2 9.4 + - - +
1523H ASN* 2.7 60.0 + - + +
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Residues in contact with LEU1520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431H TYR* 3.6 37.0 - - + -
1433H MET* 4.4 3.8 - - - -
1449H TRP* 4.1 8.1 - - + -
1466H PHE* 3.5 56.3 - - + +
1468H THR* 5.1 7.0 - - + +
1504H VAL* 5.6 0.4 - - + -
1516H VAL* 3.0 30.3 + - + +
1517H VAL* 4.0 3.4 - - + +
1519H PHE* 1.3 101.1 - - + +
1521H LYS* 1.3 63.0 + - - +
1523H ASN 4.5 1.8 - - - +
1524H GLY* 3.0 24.1 + - - +
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Residues in contact with LYS1521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428H GLU* 5.7 0.7 - - - -
1431H TYR* 3.6 25.1 - - + +
1517H VAL* 2.8 46.2 + - + +
1518H ASP* 3.4 13.5 - - + +
1519H PHE 3.2 0.2 - - - -
1520H LEU* 1.3 75.5 - - - +
1522H ARG* 1.3 65.0 + - + +
1524H GLY 3.2 13.7 - - - +
1526H THR* 5.8 0.2 - - + -
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Residues in contact with ARG1522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960B GLU* 2.9 38.4 + - - -
963B LEU* 3.3 34.2 - - - +
1518H ASP* 3.1 44.4 + - - +
1519H PHE* 4.0 6.7 - - - +
1521H LYS* 1.3 84.4 - - + +
1523H ASN* 1.3 65.3 + - - +
1524H GLY 3.3 4.8 + - - +
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Residues in contact with ASN1523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960B GLU* 2.8 28.9 + - - +
1433H MET* 3.3 28.4 - - + +
1443H VAL* 5.8 1.3 - - - +
1519H PHE* 2.7 57.2 + - + +
1520H LEU 3.8 2.0 - - - -
1522H ARG* 1.3 83.8 - - - +
1524H GLY* 1.3 54.1 + - - +
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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