Contacts of the helix formed by residues 254 - 263 (chain U) in PDB entry 2C2V
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 ASP 254 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234U GLY* 4.0 4.6 - - - -
237U SER* 4.4 13.5 + - - -
240U LEU 4.3 2.1 - - - +
241U MET* 3.4 27.9 - - + +
242U ARG* 3.0 35.3 + - - +
243U GLU* 3.3 17.4 - - - +
253U TYR* 1.3 85.9 - - - +
255U ARG* 1.3 90.7 + - - +
256U LYS* 3.5 16.2 + - - +
257U ASP* 3.6 20.3 + - - +
258U ILE* 3.3 7.6 + - - +
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Residues in contact with ARG 255 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243U GLU* 3.0 45.5 + - + +
245U CYS* 3.1 31.2 - - - -
254U ASP* 1.3 89.5 + - - +
256U LYS* 1.3 66.0 + - + +
258U ILE* 3.0 17.1 + - - +
259U GLU* 3.1 36.1 + - + +
278U GLN* 4.2 5.1 + - - +
281U LEU* 3.3 51.1 + - - +
283U PRO* 4.5 17.2 - - - +
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Residues in contact with LYS 256 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ARG* 5.7 5.9 - - - +
254U ASP* 3.8 13.8 + - - +
255U ARG* 1.3 81.2 - - + +
257U ASP* 1.3 82.2 + - - +
259U GLU* 2.8 24.7 + - - +
260U GLU* 3.1 16.6 + - - +
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Residues in contact with ASP 257 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E MET* 4.1 5.8 - - - +
236U ILE* 3.7 34.0 - - + +
237U SER* 3.7 27.7 + - - -
253U TYR* 5.6 0.9 - - + -
254U ASP* 3.8 18.7 - - + +
255U ARG 3.0 0.4 - - - -
256U LYS* 1.3 100.3 + - - +
258U ILE* 1.3 56.5 + - - +
259U GLU 2.9 4.9 + - - -
260U GLU* 3.8 4.5 + - - +
261U HIS* 3.1 15.2 + - - +
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Residues in contact with ILE 258 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236U ILE* 3.7 9.2 - - + +
245U CYS* 4.4 2.9 - - + -
253U TYR* 3.6 31.9 - - + -
254U ASP 3.3 12.1 + - - +
255U ARG* 3.0 19.2 + - - +
257U ASP* 1.3 70.6 - - - +
259U GLU* 1.3 60.9 + - - +
261U HIS* 3.9 10.1 - - + -
262U LEU* 3.1 21.9 + - + +
270U PRO* 3.1 42.8 - - + -
276U LEU* 4.8 6.5 - - + -
281U LEU* 3.7 34.5 - - + -
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Residues in contact with GLU 259 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255U ARG* 3.1 36.1 + - - +
256U LYS* 2.8 16.9 + - - +
257U ASP 2.8 5.1 - - - -
258U ILE* 1.3 80.2 - - - +
260U GLU* 1.3 58.5 + - - +
261U HIS 3.1 0.7 - - - -
262U LEU* 2.6 24.9 + - + +
263U GLN* 3.1 16.0 + - - +
278U GLN* 2.9 34.0 + - + +
281U LEU* 3.8 13.7 - - + -
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Residues in contact with GLU 260 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E MET* 3.2 43.0 - - + +
256U LYS 3.1 12.2 + - - +
257U ASP* 4.2 2.0 - - - +
259U GLU* 1.3 76.1 - - - +
261U HIS* 1.4 69.2 + - - +
262U LEU 3.0 1.0 + - - -
263U GLN* 3.1 21.7 + - - +
264U ARG* 3.1 44.2 + - - +
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Residues in contact with HIS 261 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E MET* 4.0 8.7 - - - -
101E PRO* 3.0 37.5 - - + +
236U ILE* 4.0 11.4 - - + -
257U ASP 3.1 17.5 + - - +
258U ILE* 4.3 4.7 - - + +
259U GLU 3.1 1.4 - - - -
260U GLU* 1.4 78.8 - - - +
262U LEU* 1.3 69.9 + - + +
265U VAL* 3.0 12.0 + - + +
266U GLY 2.9 19.7 + - - -
268U PHE* 2.7 55.2 + + - -
270U PRO* 3.3 26.6 - - + +
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Residues in contact with LEU 262 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258U ILE* 3.1 27.8 + - + +
259U GLU* 2.6 22.5 + - - +
261U HIS* 1.3 76.6 - - + +
263U GLN* 1.4 63.0 + - - +
266U GLY 2.9 15.9 - - - +
267U HIS* 2.6 39.7 + - + +
268U PHE 4.3 1.3 - - - +
276U LEU* 2.2 62.6 - - + +
277U THR 3.8 4.3 - - - -
278U GLN* 3.8 26.9 - - + +
281U LEU* 4.6 8.1 - - + -
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Residues in contact with GLN 263 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259U GLU 3.1 7.9 + - - +
260U GLU* 3.4 17.4 - - - +
262U LEU* 1.4 83.1 - - - +
264U ARG* 1.4 65.4 + - + +
265U VAL 2.6 18.2 + - - -
266U GLY 3.4 2.8 + - - -
267U HIS* 4.7 4.4 - - - -
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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