Contacts of the helix formed by residues 241 - 245 (chain C) in PDB entry 3V4P
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 GLN 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C PHE 5.5 0.3 - - - +
215C GLY 3.1 24.7 - - - +
216C SER* 3.4 10.3 + - - +
217C TYR* 3.8 26.6 - - + -
239C ALA 2.9 1.2 + - - -
240C PRO* 1.3 77.5 - - - +
242C HIS* 1.3 64.3 + - - +
243C GLU 3.0 1.9 + - - -
244C GLN* 3.0 47.9 + - - +
270C GLY* 6.1 0.3 - - - -
272C TYR* 3.4 29.7 + - + -
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Residues in contact with HIS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C GLN 3.7 18.8 + - - -
212C VAL* 3.5 16.2 - - - +
213C LYS* 3.9 14.4 + - + +
216C SER* 3.4 25.4 + - - +
239C ALA* 3.0 16.7 + - + +
240C PRO 3.5 1.0 - - - -
241C GLN* 1.3 74.8 - - - +
243C GLU* 1.3 86.8 + - + +
245C ILE* 3.1 2.1 + - - +
246C GLY 2.8 24.1 + - - -
247C LYS* 3.4 48.2 + - + +
249C TYR* 3.3 21.6 + - - -
265C LYS* 6.0 0.2 - - - -
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LYS* 5.6 7.8 + - + +
216C SER* 5.0 0.8 + - - -
241C GLN 3.0 3.2 + - - -
242C HIS* 1.3 93.0 + - + +
244C GLN* 1.3 64.6 + - - +
245C ILE* 2.8 30.6 + - + +
247C LYS* 4.4 6.7 + - - -
265C LYS* 3.6 28.8 + - - -
269C LEU* 4.2 2.4 - - - +
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Residues in contact with GLN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C PRO 4.6 2.1 - - - +
241C GLN* 3.0 37.8 + - - +
243C GLU* 1.3 79.2 - - - +
245C ILE* 1.3 53.7 + - - +
246C GLY 3.9 0.4 - - - -
269C LEU* 3.5 18.6 - - + -
270C GLY* 2.7 38.3 + - - +
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Residues in contact with ILE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C PRO 3.9 2.9 - - - -
242C HIS 3.9 3.6 - - - +
243C GLU* 2.8 17.4 + - + +
244C GLN* 1.3 82.1 - - - +
246C GLY* 1.3 58.6 + - - +
265C LYS* 3.7 29.6 - - - +
266C GLY* 3.5 35.0 - - - +
267C LYS 3.9 7.6 - - - +
268C LYS 3.2 25.1 - - - +
269C LEU* 4.2 11.9 - - + +
270C GLY 4.4 0.2 - - - +
271C SER* 3.7 2.8 - - - -
272C TYR 3.4 7.6 + - - -
273C PHE* 3.2 21.8 + - - +
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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