Contacts of the helix formed by residues 5261 - 5272 (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 VAL5261 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5179E SER* 3.7 17.9 - - - +
5181E GLY* 3.5 37.2 - - - +
5257E LYS* 3.4 35.2 - - + +
5259E GLY 3.6 8.9 + - - +
5260E ASP* 1.3 73.6 + - - +
5262E LYS* 1.3 65.2 + - - +
5263E PRO* 3.3 3.6 - - - -
5264E LEU* 3.2 14.7 + - + +
5265E ALA* 3.2 18.5 + - - +
5322E VAL* 4.0 19.5 - - + -
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Residues in contact with LYS5262 (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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5180E THR* 3.7 19.5 + - - +
5182E ASP* 4.5 0.4 + - - -
5260E ASP* 3.1 19.4 + - - +
5261E VAL* 1.3 80.5 - - - +
5263E PRO* 1.3 66.8 - - + +
5265E ALA* 3.1 5.3 + - - +
5266E GLU* 2.9 44.0 + - - +
5276E THR 5.7 2.2 - - - -
5278E THR* 4.3 2.6 - - - +
5279E SER* 2.6 35.2 + - - +
5282E MET* 3.1 28.7 - - + +
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Residues in contact with PRO5263 (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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5260E ASP* 3.1 33.4 - - + +
5261E VAL 3.3 4.0 - - - -
5262E LYS* 1.3 91.9 - - + +
5264E LEU* 1.3 59.7 + - - +
5266E GLU* 3.4 9.8 + - + +
5267E GLN* 3.1 22.3 + - - +
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Residues in contact with LEU5264 (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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5257E LYS* 5.7 9.6 - - + -
5261E VAL* 3.2 14.6 + - + +
5263E PRO* 1.3 76.2 - - - +
5265E ALA* 1.3 66.7 + - - +
5267E GLN* 3.2 13.1 + - - +
5268E ILE* 3.0 32.9 + - + +
5301E MET* 4.0 24.7 - - + -
5303E PHE* 5.0 0.4 - - + -
5316E GLN* 3.4 42.4 - - + +
5319E LEU* 3.4 29.8 - - + -
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Residues in contact with ALA5265 (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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5178E PHE* 3.7 27.9 - - + -
5179E SER 3.1 26.4 + - - +
5180E THR* 4.1 11.4 - - + -
5261E VAL 3.2 4.6 + - - +
5262E LYS* 3.1 10.0 + - - +
5264E LEU* 1.3 79.7 - - - +
5266E GLU* 1.3 57.9 + - - +
5268E ILE* 3.4 4.3 + - - +
5269E ALA* 2.9 29.3 + - - +
5282E MET* 4.2 8.0 - - + +
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Residues in contact with GLU5266 (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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5262E LYS* 2.9 43.4 + - - +
5263E PRO* 3.7 7.9 - - + +
5265E ALA* 1.3 73.7 - - - +
5267E GLN* 1.3 59.1 + - - +
5269E ALA* 3.6 0.3 - - - +
5270E ILE* 2.9 43.7 + - + +
5276E THR* 4.0 25.2 + - + +
5282E MET* 4.0 25.4 - - + -
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Residues in contact with GLN5267 (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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5263E PRO 3.1 13.4 + - - +
5264E LEU* 3.6 18.4 - - - +
5266E GLU* 1.3 76.8 - - - +
5268E ILE* 1.3 54.2 + - - +
5270E ILE* 3.9 8.1 - - - +
5271E THR* 2.6 40.9 + - - +
5301E MET* 4.0 27.4 - - + +
5314E GLU 5.1 6.8 + - - +
5316E GLN* 5.4 3.8 - - - +
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Residues in contact with ILE5268 (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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5174E ILE* 3.9 24.0 - - + -
5178E PHE* 4.2 27.6 - - + -
5264E LEU* 3.0 20.4 + - + +
5265E ALA* 3.6 6.3 - - - +
5267E GLN* 1.3 74.6 - - - +
5269E ALA* 1.3 66.0 + - - +
5271E THR* 3.4 4.7 + - - -
5272E ALA* 3.0 22.5 + - - +
5286E LEU* 4.6 9.9 - - + -
5294E LEU* 6.2 0.2 - - + -
5297E THR* 3.8 5.5 - - + +
5301E MET* 3.7 23.6 - - + -
5303E PHE* 4.7 1.8 - - + -
5319E LEU* 3.5 41.7 - - + -
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Residues in contact with ALA5269 (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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5265E ALA 2.9 17.9 + - - +
5266E GLU 3.3 4.2 + - - +
5268E ILE* 1.3 77.4 - - - +
5270E ILE* 1.3 56.4 + - - +
5272E ALA* 3.2 2.8 + - - -
5273E GLY 3.1 4.3 + - - -
5274E CYS* 2.7 48.1 + - + +
5276E THR* 4.1 5.6 - - + -
5282E MET* 4.0 28.0 - - + -
5286E LEU* 4.4 13.7 - - + -
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Residues in contact with ILE5270 (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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5266E GLU* 2.9 30.0 + - + +
5267E GLN* 3.9 7.4 - - - +
5269E ALA* 1.3 76.4 - - - +
5271E THR* 1.3 56.6 + - - +
5273E GLY* 2.7 24.3 + - - -
5274E CYS 3.9 7.9 - - - +
5276E THR* 3.9 20.0 - - + +
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Residues in contact with THR5271 (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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5267E GLN* 2.6 27.8 + - - +
5268E ILE 3.7 4.0 - - - -
5270E ILE* 1.3 77.6 - - - +
5272E ALA* 1.3 59.8 + - - +
5273E GLY* 3.4 0.9 + - - -
5297E THR* 3.9 18.4 + - + +
5300E LYS* 3.8 49.5 + - + +
5301E MET* 3.8 14.3 - - - -
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Residues in contact with ALA5272 (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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5268E ILE 3.0 17.6 + - - +
5269E ALA 3.6 4.9 - - - +
5270E ILE 3.1 0.6 - - - -
5271E THR* 1.3 76.2 - - - +
5273E GLY* 1.3 58.8 + - - +
5274E CYS* 4.5 1.8 - - - -
5286E LEU* 3.8 22.9 - - + -
5289E LYS* 2.8 31.1 + - + +
5293E GLU 6.2 0.2 - - - -
5294E LEU* 4.7 5.2 - - + -
5297E THR* 3.5 22.7 - - + +
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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