Contacts of the helix formed by residues 204 - 208 (chain B) in PDB entry 3RC0
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 SER 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A GLU* 4.2 0.4 - - - -
364A GLU* 3.4 12.6 - - - -
397A GLU* 4.9 1.2 + - - -
398A GLY* 3.7 23.7 + - - -
399A SER* 3.7 10.2 - - - -
134B GLN* 2.8 35.8 + - - +
203B PHE* 1.3 78.4 - - - +
205B LEU* 1.3 65.9 + - - +
206B ARG* 3.7 17.1 + - - +
207B VAL* 3.2 15.9 + - - +
208B ARG* 3.5 4.7 - - - +
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Residues in contact with LEU 205 (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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360A GLU* 3.4 17.9 + - + +
361A VAL 3.5 23.3 - - - +
362A LEU* 3.8 33.7 - - + +
364A GLU* 2.8 14.3 + - - +
482A EDO 4.4 7.4 - - - +
204B SER* 1.3 71.5 - - - +
206B ARG* 1.3 63.4 + - - +
207B VAL 3.1 1.4 + - - -
208B ARG* 3.1 55.1 + - + +
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Residues in contact with ARG 206 (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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364A GLU* 4.5 0.6 + - - -
365A GLU* 4.0 35.7 + - + +
395A ARG* 5.7 8.1 - - - +
397A GLU* 2.9 35.9 + - - +
482A EDO 4.0 16.4 + - - +
204B SER* 3.3 11.7 + - - +
205B LEU* 1.3 78.0 - - - +
207B VAL* 1.3 62.2 + - + +
208B ARG 3.7 0.2 + - - -
209B SER* 4.4 10.0 - - - -
212B LEU* 4.4 4.5 - - - +
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Residues in contact with VAL 207 (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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397A GLU* 5.6 0.7 - - - +
130B LEU* 3.7 38.6 - - + +
133B LEU* 4.8 7.4 - - + -
134B GLN* 3.6 40.2 - - + +
196B MET* 3.8 11.9 - - - +
203B PHE* 4.1 13.7 - - + -
204B SER* 3.2 19.3 - - - +
205B LEU 3.1 0.2 - - - -
206B ARG* 1.3 82.6 - - + +
208B ARG* 1.3 59.8 + - - +
209B SER 3.1 8.6 + - - +
212B LEU* 3.8 17.9 - - + +
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Residues in contact with ARG 208 (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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360A GLU* 2.9 29.9 + - - -
188B TYR* 3.3 8.4 + - - -
193B LEU* 4.2 9.0 - - + -
196B MET* 3.7 42.5 + - + -
197B GLU* 3.9 28.3 + - - +
200B PRO* 3.3 18.4 - - - +
203B PHE* 2.9 27.0 + - - +
204B SER 3.5 11.0 + - - +
205B LEU* 3.1 34.5 + - - +
206B ARG 3.4 0.2 - - - -
207B VAL* 1.3 75.1 - - - +
209B SER* 1.3 59.4 + - - +
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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