Contacts of the helix formed by residues 1323 - 1327 (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 ASP1323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825C PRO 3.6 7.8 - - - +
826C ARG* 5.4 3.1 + - - -
827C ASN* 4.7 10.1 + - - +
830C GLN* 3.3 27.6 + - - +
1322D THR* 1.3 63.7 - - - +
1324D PHE* 1.3 54.6 + - - -
1326D GLY* 3.9 3.1 - - - -
1328D VAL 2.8 39.7 + - - +
1329D ASP* 3.4 16.8 - - - +
1330D GLY* 3.5 20.1 + - - -
1331D LEU 2.8 19.8 + - - -
1332D ASN* 3.0 8.9 + - - +
2358G MET 2.8 12.4 - - - +
2359G PRO* 3.0 21.1 - - + +
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Residues in contact with PHE1324 (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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1321D ASN* 3.1 12.0 + - - -
1322D THR 3.1 3.0 + - - -
1323D ASP* 1.3 76.7 - - - +
1325D PHE* 1.3 72.7 + + - +
1327D LEU 2.9 8.0 + - - -
1328D VAL* 4.1 23.3 - - + -
1331D LEU* 3.6 18.9 + - + +
1333D PHE* 3.8 25.8 - + + -
2357G ARG* 2.2 85.6 - - + +
2358G MET 2.8 8.7 + - - +
2364G GLN* 4.9 0.2 + - - -
2366G PHE* 5.1 7.4 - + + -
2367G GLY 6.0 0.7 - - - -
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Residues in contact with PHE1325 (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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1273D VAL* 4.8 0.2 - - + -
1321D ASN* 3.3 8.2 + - - -
1324D PHE* 1.3 74.7 - + - +
1326D GLY* 1.3 5.6 - - - +
1327D LEU* 3.1 1.7 - - - +
2356G PRO* 4.9 2.0 - - + -
2357G ARG* 0.6 160.9 - - + +
2358G MET* 0.8 223.6 + - + +
2359G PRO 2.1 21.2 + - - -
2360G ARG* 0.8 178.6 - - - -
2366G PHE* 3.7 31.4 - + - -
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Residues in contact with GLY1326 (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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823C ARG* 3.0 33.2 + - - +
1272D ASP* 4.4 1.8 - - - -
1323D ASP* 3.4 5.8 - - - -
1325D PHE* 1.3 11.1 - - - +
1327D LEU* 1.3 56.0 + - - +
1328D VAL 3.7 0.7 - - - -
1329D ASP* 5.3 0.2 - - - -
2358G MET* 0.5 155.2 + - - +
2359G PRO* 1.6 26.6 - - - +
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Residues in contact with LEU1327 (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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823C ARG* 4.0 16.1 - - - +
824C MET 5.6 0.3 + - - -
1324D PHE 2.9 6.7 + - - +
1325D PHE 3.1 3.1 - - - +
1326D GLY 1.3 69.4 - - - +
1328D VAL* 1.3 66.1 + - + +
1329D ASP 4.1 0.9 - - - -
2355G THR* 4.7 9.4 - - + -
2356G PRO 3.1 12.8 - - - +
2357G ARG* 2.6 47.8 - - - +
2358G MET* 2.1 46.6 + - + +
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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