Contacts of the helix formed by residues 5172 - 5178 (chain E) in PDB entry 2H7C
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 LEU5172 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5087E CYS* 4.0 17.1 - - + +
5088E THR 4.3 7.8 - - - +
5089E GLN* 3.5 29.2 - - + +
5140E HIS* 4.1 4.3 - - + +
5144E LEU 3.6 14.6 - - - +
5145E MET 3.7 9.2 - - - +
5146E VAL* 3.6 28.0 - - - +
5147E GLY 3.6 7.4 - - - +
5170E TYR* 3.4 45.5 - - + +
5171E ARG* 1.3 74.8 - - - +
5173E GLY* 1.3 69.5 + - - +
5174E ILE 3.4 0.2 + - - -
5175E TRP* 3.2 19.9 + - - +
5176E GLY* 3.0 10.0 + - - -
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Residues in contact with GLY5173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5144E LEU 2.8 14.1 + - - -
5145E MET* 3.6 34.2 + - - +
5172E LEU* 1.3 72.6 - - - +
5174E ILE* 1.3 54.8 + - - -
5175E TRP* 5.0 2.5 - - - -
5176E GLY 3.1 0.3 + - - -
5177E PHE* 2.7 38.9 + - - +
5178E PHE 4.0 0.2 + - - -
5319E LEU* 3.8 8.1 - - - -
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Residues in contact with ILE5174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5065E PHE* 3.3 23.8 - - + -
5145E MET* 5.0 0.6 - - - +
5172E LEU 3.4 0.6 + - - -
5173E GLY* 1.3 70.3 - - - -
5175E TRP* 1.3 75.1 + - + +
5178E PHE* 3.0 38.9 + - + +
5268E ILE* 3.9 26.2 - - + -
5286E LEU* 5.4 1.8 - - + -
5294E LEU* 4.0 28.3 - - + +
5297E THR* 4.1 13.0 - - + -
5298E THR* 3.7 25.7 + - - +
5303E PHE* 4.7 6.7 - - + -
5319E LEU* 3.4 24.8 - - + +
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Residues in contact with TRP5175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5059E PRO 6.0 0.9 - - - -
5064E ARG* 4.1 20.3 - - + +
5065E PHE* 4.2 11.9 + - - -
5087E CYS* 6.5 0.9 - - + -
5088E THR* 3.3 52.9 - - + -
5089E GLN* 4.7 3.4 - - - -
5114E GLU* 2.8 36.3 + - + +
5171E ARG* 3.7 28.0 + - + -
5172E LEU 3.2 14.9 + - - +
5173E GLY* 5.5 1.3 - - - -
5174E ILE* 1.3 85.2 - - + +
5176E GLY* 1.3 59.0 + - - +
5189E TRP* 3.6 13.7 - - - +
5291E GLU* 3.7 10.3 - - + -
5294E LEU* 3.5 32.0 - - + +
5295E LEU* 3.8 20.9 - - + -
5298E THR* 3.9 15.7 - - + -
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Residues in contact with GLY5176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5171E ARG* 3.4 31.4 - - - +
5172E LEU 3.0 10.7 + - - -
5173E GLY 3.7 1.1 - - - -
5175E TRP* 1.3 80.1 - - - +
5177E PHE* 1.3 66.4 + - - +
5189E TRP* 2.8 31.1 + - - -
5190E GLY 2.8 7.0 + - - -
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Residues in contact with PHE5177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5144E LEU* 3.8 43.1 - - + -
5170E TYR* 4.6 3.6 - + - -
5171E ARG 3.3 19.5 - - - -
5173E GLY 2.7 22.6 + - - +
5176E GLY* 1.3 80.7 - - - +
5178E PHE* 1.3 65.4 + - - +
5179E SER* 3.2 9.5 + - - -
5187E GLY* 4.6 1.0 - - - -
5188E ASN* 4.0 15.4 + - - +
5189E TRP* 4.4 0.2 - - - -
5190E GLY* 3.7 15.3 - - - -
5191E HIS* 3.7 36.3 - + - -
5319E LEU* 3.8 31.5 - - + +
5320E GLY* 3.6 31.2 + - - +
5321E THR 4.1 0.2 - - - -
5322E VAL* 5.1 1.0 - - - +
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Residues in contact with PHE5178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5065E PHE* 3.6 21.1 - + + -
5174E ILE* 3.0 27.3 + - + +
5176E GLY 3.9 0.6 - - - -
5177E PHE* 1.3 75.9 - - - +
5179E SER* 1.3 62.5 + - - +
5180E THR* 3.7 31.4 - - + -
5185E SER* 3.2 20.2 + - - -
5187E GLY* 3.6 2.4 - - - -
5189E TRP* 3.2 21.5 + - - -
5265E ALA* 3.7 35.0 - - + -
5268E ILE* 4.2 23.3 - - + -
5282E MET* 4.9 6.5 - - + -
5283E VAL* 3.9 11.7 - - + -
5286E LEU* 3.2 34.8 - - + -
5319E LEU* 5.4 5.8 - - - -
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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