Contacts of the helix formed by residues 2060 - 2064 (chain B) 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 LEU2060 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2058B PRO* 2.8 31.3 + - + +
2059B PRO* 1.3 76.5 - - - +
2061B GLY* 1.3 68.2 + - - +
2062B PRO* 3.3 4.0 - - - +
2063B LEU* 3.0 19.3 + - - +
2064B ARG* 5.5 0.7 - - - +
2114B GLU* 3.5 48.7 - - + +
2115B ASP* 4.1 5.6 - - + +
385C SO4 4.0 9.1 + - - +
3280C ALA* 3.7 18.6 - - + +
3281C VAL* 4.5 6.3 - - + +
3284C HIS* 3.7 39.3 - - + +
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Residues in contact with GLY2061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B SO4 5.2 3.2 + - - -
2060B LEU* 1.3 73.0 - - - +
2062B PRO* 1.3 70.2 - - - +
2063B LEU 3.2 1.0 + - - -
2064B ARG* 3.2 24.9 + - - +
2287B ARG* 4.3 16.7 - - - +
385C SO4 3.9 0.2 - - - -
3284C HIS* 3.6 24.0 + - - -
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Residues in contact with PRO2062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B SO4 4.2 18.3 + - - +
2060B LEU 3.6 4.0 - - - +
2061B GLY* 1.3 82.8 - - - +
2063B LEU* 1.3 67.7 - - + +
2064B ARG 3.2 2.5 + - - -
2066B THR* 3.4 16.1 - - - +
2287B ARG* 3.5 12.4 + - - -
385C SO4 4.0 12.6 - - - +
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Residues in contact with LEU2063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2057B LYS* 3.8 34.1 - - + +
2058B PRO 3.5 20.6 - - - +
2059B PRO* 3.7 15.5 - - + +
2060B LEU 3.0 14.1 + - - +
2062B PRO* 1.3 83.7 - - + +
2064B ARG* 1.3 63.6 + - - +
2065B PHE 3.5 0.3 + - - -
2066B THR* 2.8 32.0 + - + +
2067B PRO 5.2 0.7 - - - +
2069B GLN* 3.7 33.4 - - + +
2171B ARG* 3.7 9.7 + - - -
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Residues in contact with ARG2064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B SO4 2.8 21.8 + - - -
2059B PRO 3.9 14.9 + - - +
2060B LEU* 6.1 0.4 - - - +
2061B GLY* 3.2 21.0 + - - +
2062B PRO 3.2 1.0 - - - -
2063B LEU* 1.3 79.9 - - - +
2065B PHE* 1.3 99.2 + - + +
2114B GLU* 2.7 30.9 + - - -
2171B ARG* 4.7 3.1 - - - +
2175B TRP* 4.0 14.5 - - + +
2286B LEU 2.9 20.4 + - - -
2287B ARG* 2.7 45.0 + - + +
2289B LYS 2.7 26.9 + - - -
2290B THR 4.2 0.2 - - - -
2291B GLU 4.1 3.4 - - - +
2294B LEU* 3.2 17.7 - - - +
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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