Contacts of the helix formed by residues 1351 - 1358 (chain A) 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 ASN1351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1182A ASP* 3.5 29.1 + - - +
1183A ARG* 3.7 17.8 - - - +
1349A THR 3.6 2.6 + - - -
1350A SER* 1.3 69.3 - - - +
1352A THR* 1.3 60.1 + - - +
1353A LEU* 2.9 23.7 + - - +
1354A GLU* 3.0 39.5 + - + +
1355A GLU* 2.9 27.6 + - - +
1374A ASN* 4.1 7.4 + - - +
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Residues in contact with THR1352 (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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1182A ASP 3.2 19.3 + - - -
1183A ARG* 3.9 2.9 - - - -
1184A LEU* 3.2 37.8 + - + -
1185A VAL* 3.8 14.4 + - + +
1350A SER 3.3 4.1 + - - -
1351A ASN* 1.3 70.4 + - - +
1353A LEU* 1.3 64.3 + - - +
1355A GLU* 3.6 6.4 - - - +
1356A PHE* 3.0 48.6 + - + -
1365A MET* 3.4 18.4 - - + +
1377A MET* 5.1 0.7 - - - +
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Residues in contact with LEU1353 (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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1117A GLU* 6.1 0.2 - - - +
1181A PHE 5.3 3.4 - - - +
1182A ASP* 3.8 23.9 + - - +
1184A LEU* 3.7 25.8 - - + -
1351A ASN* 2.9 10.6 + - - +
1352A THR* 1.3 79.0 - - - +
1354A GLU* 1.3 58.4 + - + +
1356A PHE* 3.6 14.0 + - + +
1357A GLU* 3.2 23.6 + - - +
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Residues in contact with GLU1354 (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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1351A ASN* 3.0 37.5 + - + +
1353A LEU* 1.3 76.0 - - + +
1355A GLU* 1.3 61.1 + - - +
1356A PHE 3.3 0.4 - - - -
1357A GLU* 3.2 22.2 + - - +
1358A HIS* 2.7 39.4 + - + +
1374A ASN* 4.1 20.1 + - - +
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Residues in contact with GLU1355 (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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1350A SER* 4.3 7.9 - - - +
1351A ASN 2.9 18.9 + - - +
1352A THR 3.3 7.4 + - - +
1354A GLU* 1.3 72.6 - - - +
1356A PHE* 1.3 67.2 + - - +
1358A HIS* 3.1 10.8 + - - +
1359A GLY 3.4 0.3 + - - -
1360A ARG* 3.0 33.0 + - + +
1365A MET* 3.4 54.4 - - + +
1367A ARG* 2.7 34.9 + - - -
1374A ASN* 2.9 27.4 + - - +
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Residues in contact with PHE1356 (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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398A LYS* 4.7 6.4 - - - -
1105A LEU* 4.3 21.8 - - + -
1184A LEU* 4.2 11.7 - - + -
1185A VAL* 4.8 0.9 - - + -
1352A THR* 3.0 41.9 + - + +
1353A LEU* 3.6 17.0 - - + +
1355A GLU* 1.3 72.7 - - - +
1357A GLU* 1.3 57.2 + - - +
1358A HIS 2.9 4.9 - - - -
1359A GLY* 2.9 20.6 + - - -
1360A ARG 3.4 21.1 - - - +
1362A PRO* 4.4 17.3 - - + -
1365A MET* 4.5 5.4 - - - -
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Residues in contact with GLU1357 (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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395A SER* 4.7 1.7 + - - -
397A LYS* 3.2 57.1 + - + +
398A LYS* 4.0 10.7 - - - +
1353A LEU 3.2 11.2 + - - +
1354A GLU* 3.2 25.2 + - - +
1356A PHE* 1.3 77.5 - - - +
1358A HIS* 1.3 61.2 + - - +
1359A GLY 3.4 0.4 - - - -
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Residues in contact with HIS1358 (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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397A LYS* 3.4 61.2 - - + +
398A LYS* 3.6 6.2 - - - -
400A ARG* 3.4 20.6 + - - -
1354A GLU* 2.7 33.9 + - + +
1355A GLU* 3.1 11.9 + - - +
1356A PHE 2.9 0.8 - - - -
1357A GLU* 1.3 84.0 - - - +
1359A GLY* 1.3 60.8 + - - +
1360A ARG* 3.5 11.5 + - + +
1367A ARG* 5.8 1.6 - - - +
1372A THR* 5.3 13.6 - - + +
1374A ASN* 6.2 0.4 + - - -
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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