Contacts of the helix formed by residues 5290 - 5302 (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 THR5290 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484D SO4 3.4 17.0 - - - +
4288D GLN* 6.1 1.3 - - - +
5064E ARG* 4.2 1.1 - - - -
5288E GLN 4.9 3.8 - - - +
5289E LYS* 1.3 77.9 - - - +
5291E GLU* 1.3 65.5 + - - +
5292E GLU* 3.5 9.7 + - - +
5293E GLU* 3.0 46.0 + - - +
5294E LEU* 3.1 13.0 + - - +
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Residues in contact with GLU5291 (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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484D SO4 2.9 17.6 + - - +
4275D LYS* 4.9 14.4 + - - +
5064E ARG* 4.5 0.2 - - - +
5088E THR* 2.5 40.2 + - + +
5112E LEU* 4.2 5.3 - - - +
5113E SER* 3.2 11.5 + - - -
5114E GLU* 3.1 46.0 + - + +
5175E TRP* 3.7 6.6 - - + -
5290E THR* 1.3 71.5 - - - +
5292E GLU* 1.3 58.9 + - - +
5294E LEU* 3.3 0.7 + - - -
5295E LEU* 3.0 28.6 + - + +
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Residues in contact with GLU5292 (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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3300C LYS* 3.0 37.2 + - - +
4275D LYS* 5.0 10.7 + - - +
5290E THR* 3.1 9.0 + - - +
5291E GLU* 1.3 81.4 - - - +
5293E GLU* 1.3 57.4 - - + +
5295E LEU* 3.3 22.9 + - - +
5296E GLU* 2.8 42.6 + - - +
5299E LEU* 6.1 0.2 - - - +
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Residues in contact with GLU5293 (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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5288E GLN 4.7 0.5 - - - +
5289E LYS* 3.4 32.3 + - + +
5290E THR* 3.0 44.5 + - - +
5292E GLU* 1.3 76.7 - - + +
5294E LEU* 1.3 59.0 + - - +
5296E GLU* 3.3 18.8 + - - +
5297E THR* 3.0 30.2 + - - -
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Residues in contact with LEU5294 (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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5064E ARG* 3.1 43.7 - - - +
5065E PHE* 4.6 7.4 - - + -
5174E ILE* 4.0 16.8 - - + +
5175E TRP* 3.5 29.4 - - + +
5272E ALA* 4.7 1.1 - - + -
5286E LEU* 3.9 22.4 - - + +
5289E LYS* 3.8 23.8 - - + -
5290E THR 3.1 9.8 + - - +
5291E GLU 3.9 1.8 - - - +
5293E GLU* 1.3 75.3 - - - +
5295E LEU* 1.3 61.3 + - - +
5297E THR* 3.3 14.1 + - + +
5298E THR* 3.0 28.8 + - - -
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Residues in contact with LEU5295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5088E THR* 4.3 12.6 - - + -
5089E GLN* 3.7 26.2 - - - +
5090E ASP* 4.0 2.0 - - - +
5091E PRO* 4.5 7.0 - - + -
5112E LEU* 4.1 24.0 - - + -
5175E TRP* 3.8 10.3 - - + -
5291E GLU* 3.0 17.5 + - + +
5292E GLU* 3.7 25.6 - - - +
5293E GLU 3.2 0.2 - - - -
5294E LEU* 1.3 74.4 - - - +
5296E GLU* 1.3 65.9 + - - +
5298E THR* 3.1 8.9 + - - -
5299E LEU* 3.0 51.1 + - + +
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Residues in contact with GLU5296 (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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3296C GLU* 2.9 47.4 - - + +
3300C LYS* 3.5 25.6 + - - -
5292E GLU* 2.8 42.1 + - - +
5293E GLU* 3.5 22.6 - - - +
5294E LEU 3.3 0.2 - - - -
5295E LEU* 1.3 77.6 - - - +
5297E THR* 1.3 57.2 + - - +
5299E LEU* 3.3 10.8 + - - +
5300E LYS* 2.9 36.5 + - - +
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Residues in contact with THR5297 (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* 4.1 16.4 - - + -
5268E ILE* 3.8 24.0 - - + +
5271E THR* 3.9 17.9 + - + -
5272E ALA* 3.5 24.6 - - + +
5293E GLU 3.0 16.4 + - - -
5294E LEU* 3.4 13.0 - - + -
5295E LEU 3.2 0.2 - - - -
5296E GLU* 1.3 78.1 - - - +
5298E THR* 1.3 62.3 + - - +
5300E LYS* 3.2 8.4 + - - +
5301E MET* 2.9 34.5 + - + +
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Residues in contact with THR5298 (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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5E COA 5.7 2.5 - - - +
5089E GLN* 5.8 1.8 - - - -
5090E ASP* 5.1 10.3 - - + +
5145E MET* 4.4 11.0 - - + -
5174E ILE* 3.7 15.0 + - - +
5175E TRP* 3.9 15.5 - - + -
5294E LEU 3.0 15.0 + - - -
5295E LEU* 3.1 17.2 + - + -
5297E THR* 1.3 76.9 - - - +
5299E LEU* 1.3 69.4 + - + +
5301E MET* 3.2 13.2 + - - +
5302E LYS 3.4 7.6 + - - -
5303E PHE* 3.8 30.5 + - + -
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Residues in contact with LEU5299 (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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3C COA 2.9 19.8 + - - +
3299C LEU* 4.8 11.2 - - + +
3300C LYS* 4.0 39.0 - - + +
5E COA 4.2 22.9 + - - +
5090E ASP* 4.2 22.2 - - + +
5091E PRO* 5.2 3.6 - - + -
5295E LEU* 3.0 41.9 + - + +
5296E GLU* 3.6 12.8 - - - +
5298E THR* 1.3 80.6 - - + +
5300E LYS* 1.3 60.6 + - + +
5302E LYS* 3.2 10.3 + - - +
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Residues in contact with LYS5300 (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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3C COA 4.0 7.7 + - - -
3092C LYS* 2.9 29.4 + - - +
3292C GLU* 3.6 19.8 + - - +
3295C LEU* 5.9 6.2 - - - +
3296C GLU* 3.4 38.8 + - - +
3299C LEU* 3.9 20.4 - - + -
5271E THR* 3.8 35.7 + - + +
5296E GLU* 2.9 24.3 + - + +
5297E THR* 3.6 4.9 - - - +
5299E LEU* 1.3 77.1 - - - +
5301E MET* 1.3 60.2 + - - +
5302E LYS 3.3 1.2 + - - -
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Residues in contact with MET5301 (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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3092C LYS* 4.6 2.4 - - - +
5174E ILE* 5.4 0.4 - - + -
5264E LEU* 4.0 13.0 - - + -
5267E GLN* 4.0 22.4 - - + +
5268E ILE* 3.7 23.8 - - + -
5271E THR* 3.8 24.5 - - + -
5297E THR* 2.9 32.2 + - + +
5298E THR 3.2 3.3 + - - +
5300E LYS* 1.3 75.3 - - - +
5302E LYS* 1.3 80.6 + - - +
5303E PHE* 3.3 54.8 + - + -
5316E GLN* 5.1 3.6 - - + +
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Residues in contact with LYS5302 (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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3C COA 2.6 35.2 - - + +
3092C LYS* 3.2 42.4 - - + +
5E COA 3.2 6.0 + - - -
5298E THR 3.4 2.4 + - - -
5299E LEU* 3.2 10.8 + - - +
5300E LYS 3.2 3.3 - - - +
5301E MET* 1.3 95.9 - - - +
5303E PHE* 1.3 67.3 + - - +
5305E SER* 3.6 16.3 + - - +
5307E ASP* 2.8 51.4 + - + -
5309E GLN* 5.3 3.2 - - - +
5315E SER* 6.6 0.2 - - - +
5317E PRO* 5.1 1.4 - - - +
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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