Contacts of the helix formed by residues 1512 - 1519 (chain D) in PDB entry 2ZLE
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 ASN1512 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1480D GLU* 3.8 13.3 + - - -
1510D ASP* 3.1 14.9 + - - +
1511D ASP* 1.3 73.8 - - - +
1513D GLN* 1.3 64.5 + - - +
1514D PHE* 3.1 10.0 + - - +
1515D THR* 2.8 38.7 + - - +
1516D ARG* 3.0 35.9 + - - +
4140K GLU* 2.9 47.7 + - + +
4144K ALA* 5.7 0.2 - - - -
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Residues in contact with GLN1513 (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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1477D TYR* 5.5 2.5 - - + -
1512D ASN* 1.3 74.5 - - - +
1514D PHE* 1.3 57.8 + - - +
1516D ARG* 3.2 34.8 + - - +
1517D ASP* 2.8 64.6 + - - +
2952H GLU* 4.5 5.1 + - - +
2953H LEU* 6.2 0.6 - - - +
4140K GLU* 5.5 3.6 - - + +
4143K LYS* 5.4 5.9 + - + +
4144K ALA* 5.0 12.9 - - + +
4146K LYS* 6.1 3.2 - - - +
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Residues in contact with PHE1514 (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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1435D VAL* 3.3 34.8 - - + -
1438D LEU* 4.2 10.1 - - + -
1473D LEU* 3.9 16.8 - - + -
1477D TYR* 3.7 38.5 - + + -
1480D GLU* 3.7 38.6 - - + +
1481D ASP 3.4 23.6 - - - -
1482D ILE* 4.4 4.9 - - + -
1512D ASN* 3.1 7.5 + - - +
1513D GLN* 1.3 79.0 - - - +
1515D THR* 1.3 66.5 + - + +
1517D ASP* 3.3 3.3 + - - +
1518D ALA* 3.0 28.5 + - + +
1520D ILE* 4.1 15.5 - - + -
4736M ARG* 5.2 0.7 - - + -
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Residues in contact with THR1515 (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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1481D ASP 4.8 3.6 - - - +
1509D LEU* 4.7 13.2 - - + -
1510D ASP 3.6 13.1 + - - +
1511D ASP* 3.9 2.9 + - - -
1512D ASN* 2.8 42.4 + - - +
1514D PHE* 1.3 88.0 - - + +
1516D ARG* 1.3 56.9 + - - +
1518D ALA* 4.7 1.3 - - - -
1519D GLY* 2.9 24.1 + - - -
1520D ILE* 3.0 30.0 + - + +
1522D THR* 3.7 24.2 - - + +
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Residues in contact with ARG1516 (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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1511D ASP* 3.4 30.1 + - - +
1512D ASN* 3.0 14.9 + - - +
1513D GLN* 3.2 52.7 + - - +
1515D THR* 1.3 78.1 + - - +
1517D ASP* 1.3 63.6 + - - +
1519D GLY* 3.3 11.7 + - - -
2952H GLU* 2.7 57.8 + - - +
4141K LEU* 6.1 0.4 - - - +
4144K ALA* 3.0 32.5 - - - +
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Residues in contact with ASP1517 (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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1437D SER* 4.0 6.8 + - - -
1438D LEU* 3.9 16.2 - - + +
1477D TYR* 2.9 36.7 + - + +
1513D GLN* 2.8 49.0 + - - +
1514D PHE 3.6 4.5 - - - +
1516D ARG* 1.3 73.9 - - - +
1518D ALA* 1.3 59.8 + - - +
1519D GLY 3.5 0.2 + - - -
2762H PHE 4.2 1.6 - - - +
2763H GLY 4.3 1.8 - - - -
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Residues in contact with ALA1518 (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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1435D VAL* 3.7 22.9 - - + +
1436D GLY* 3.5 2.9 - - - -
1437D SER* 3.2 24.1 + - - -
1438D LEU* 3.8 18.6 - - + -
1514D PHE* 3.0 16.6 + - + +
1515D THR 4.2 0.2 - - - +
1517D ASP* 1.3 76.7 - - - +
1519D GLY* 1.3 61.7 + - - +
1520D ILE* 3.8 23.6 - - + -
2761H PHE* 3.5 6.4 - - - -
3550J PHE* 3.7 0.2 - - - -
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Residues in contact with GLY1519 (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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1515D THR 2.9 7.5 + - - -
1516D ARG 3.3 11.0 + - - -
1517D ASP 3.3 0.6 + - - -
1518D ALA* 1.3 74.5 - - - +
1520D ILE* 1.3 51.7 + - - +
3550J PHE* 1.2 84.4 - - - -
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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