Contacts of the helix formed by residues 243 - 247 (chain A) in PDB entry 2R92
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 PRO 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 3.0 35.9 - - + -
79A GLY* 3.2 28.3 - - - -
80A HIS 3.2 6.1 - - - +
81A PHE* 3.8 22.2 - - + +
241A VAL 3.3 4.2 - - - +
242A PRO* 1.3 91.2 - - + +
244A PRO* 1.3 73.5 - - + +
245A PRO* 5.0 0.9 - - + -
246A VAL* 3.1 24.0 + - + +
247A ARG* 3.8 5.0 + - - +
1205B GLN* 4.0 5.4 - - - +
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Residues in contact with PRO 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN* 4.9 9.4 - - + +
58A LEU* 3.5 21.1 - - + -
59A GLY* 3.7 24.7 - - - -
60A SER* 3.9 12.3 - - - +
61A ILE* 5.4 5.8 - - + -
243A PRO* 1.3 84.9 - - + +
245A PRO* 1.3 67.1 - - + +
246A VAL 2.5 15.9 + - - -
247A ARG* 2.6 34.3 + - - +
248A PRO* 2.8 16.7 - - + -
249A SER 6.0 0.2 - - - +
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Residues in contact with PRO 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY* 5.4 1.3 - - - -
60A SER 5.4 2.2 - - - +
74A MET* 5.5 6.1 - - - +
77A CYS 4.8 10.1 - - - +
79A GLY* 4.7 8.5 - - - +
243A PRO* 3.9 4.7 - - + -
244A PRO* 1.3 99.7 - - + +
246A VAL* 1.3 61.8 + - + +
248A PRO* 3.6 16.2 - - + +
1113B VAL 5.4 0.7 - - - +
1114B LEU* 3.8 15.1 - - - +
1116B ARG* 5.6 2.5 - - - +
1198B TYR* 3.6 12.5 + - - +
1201B LYS* 3.5 28.9 - - - +
1202B LEU* 4.7 3.8 - - - +
1205B GLN* 5.0 2.5 - - - +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A PRO* 3.7 27.6 - - + -
243A PRO* 3.6 22.7 - - + +
244A PRO 2.5 7.3 + - - -
245A PRO* 1.3 74.2 - - - +
247A ARG* 1.3 53.0 + - + +
248A PRO* 3.5 0.9 - - - -
262A LEU* 4.7 5.6 - - + -
325A ILE* 6.2 0.9 - - + -
328A ARG* 2.4 41.4 + - - +
1114B LEU* 3.5 9.2 - - - +
1202B LEU* 3.9 7.0 - - + -
1205B GLN* 3.9 27.8 - - + +
1206B GLU* 3.8 28.7 - - + -
1209B ALA* 5.6 0.9 - - + -
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.4 27.3 - - - +
54A ASN* 3.6 28.9 + - - +
58A LEU* 4.3 2.8 - - - +
241A VAL* 4.2 8.3 - - - +
242A PRO* 2.9 28.7 + - - +
243A PRO* 3.8 12.6 - - - +
244A PRO* 2.6 20.6 + - - +
246A VAL* 1.3 75.0 - - + +
248A PRO* 1.3 70.1 - - - +
259A GLU* 4.8 2.4 + - - +
260A ASP* 3.5 13.3 + - - +
262A LEU* 3.8 26.9 - - + -
263A THR* 3.2 45.3 + - - +
266A LEU* 3.9 13.3 - - - +
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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