Contacts of the helix formed by residues 5060 - 5064 (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 LEU5060 (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 5.0 3.1 - - - +
485D SO4 4.0 11.2 + - - +
4280D ALA* 3.8 29.6 - - + +
4281D VAL* 4.6 5.8 - - + +
4284D HIS* 3.8 25.8 - - + +
5058E PRO* 2.8 32.7 + - + +
5059E PRO* 1.3 76.6 - - - +
5061E GLY* 1.3 69.9 + - - +
5062E PRO* 3.2 4.2 - - - +
5063E LEU* 3.0 17.5 + - - +
5064E ARG* 6.1 0.4 - - - +
5114E GLU* 3.7 46.9 - - + +
5115E ASP* 4.1 5.8 - - + +
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Residues in contact with GLY5061 (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 5.4 3.7 + - - -
4284D HIS* 3.6 21.8 + - - -
5060E LEU* 1.3 72.7 - - - +
5062E PRO* 1.3 70.2 - - - +
5063E LEU 3.1 1.4 + - - -
5064E ARG* 3.2 25.1 + - - +
5114E GLU* 5.8 0.2 + - - -
5287E ARG* 4.4 17.4 - - - +
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Residues in contact with PRO5062 (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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485D SO4 4.2 10.8 - - - +
585E SO4 4.5 12.9 + - - +
5060E LEU 3.5 4.7 - - - +
5061E GLY* 1.3 82.4 - - - +
5063E LEU* 1.3 67.2 + - + +
5064E ARG 3.2 3.5 + - - +
5066E THR* 3.3 19.2 - - - +
5287E ARG* 3.9 16.4 + - + -
6062F PRO* 6.5 0.4 - - + -
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Residues in contact with LEU5063 (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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5057E LYS* 3.8 36.3 - - + +
5058E PRO 3.5 20.4 - - - +
5059E PRO* 3.7 15.1 - - + +
5060E LEU 3.0 13.6 + - - +
5062E PRO* 1.3 85.1 - - + +
5064E ARG* 1.3 62.5 + - - +
5065E PHE 3.5 0.3 + - - -
5066E THR* 2.6 33.6 + - + +
5067E PRO 5.2 0.2 - - - +
5069E GLN* 3.7 32.3 - - + +
5171E ARG* 3.5 10.4 + - - -
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Residues in contact with ARG5064 (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 2.7 26.3 + - - -
5059E PRO 3.9 15.4 + - - +
5060E LEU* 6.1 0.6 - - - +
5061E GLY* 3.2 22.6 + - - +
5063E LEU* 1.3 80.3 - - - +
5065E PHE* 1.3 98.4 + - + +
5066E THR* 3.5 0.2 - - - +
5114E GLU* 2.7 31.7 + - - -
5171E ARG* 4.5 2.9 - - - +
5175E TRP* 4.1 14.3 - - + +
5286E LEU 2.8 24.0 + - - -
5287E ARG* 2.8 41.7 + - + +
5289E LYS 2.9 18.2 + - - -
5290E THR 4.2 0.2 - - - -
5291E GLU 4.2 2.8 - - - +
5294E LEU* 3.1 16.6 - - - +
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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