Contacts of the strand formed by residues 205 - 209 (chain C) in PDB entry 2R6C
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 LEU 205 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C SER 4.1 0.8 + - - -
204C ASP* 1.3 71.2 - - - +
206C ILE* 1.3 66.3 + - - +
207C ILE* 4.6 3.6 - - + +
322C LEU* 6.3 0.4 - - + -
343C SER* 3.9 14.1 - - - +
346C LEU* 4.3 14.8 - - + +
347C LYS* 3.7 46.3 - - + +
350C ALA* 4.4 1.5 - - + +
357C VAL* 3.5 14.8 - - + +
359C ALA* 4.0 24.2 - - + -
386C ILE* 6.3 0.7 - - + -
389C ASP* 4.0 3.4 - - + +
390C ALA* 3.6 24.9 - - + +
391C ASP* 2.7 34.2 + - - +
392C ILE 3.6 4.0 + - - +
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 3.2 49.4 - - + -
204C ASP* 4.2 9.2 - - + +
205C LEU* 1.3 71.9 - - - +
207C ILE* 1.3 63.0 + - - +
208C VAL* 4.5 15.7 - - + -
356C PRO* 3.7 26.5 - - + -
357C VAL 2.7 12.0 + - - +
358C ILE* 3.1 20.9 - - + +
359C ALA 2.8 25.9 + - - +
392C ILE* 3.3 38.1 - - + +
394C ALA* 5.2 3.4 - - + -
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Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU* 3.9 3.1 + - + -
206C ILE* 1.3 73.7 - - - +
208C VAL* 1.3 58.4 + - - +
209C ALA* 4.8 1.1 - - + +
322C LEU* 4.3 7.9 - - + -
359C ALA* 3.0 17.7 - - + +
361C SER* 3.7 27.8 - - - -
380C ILE* 4.1 10.3 - - + -
386C ILE* 3.3 35.2 - - + -
390C ALA* 3.4 30.5 - - + -
392C ILE 2.9 7.7 + - - +
393C VAL* 3.4 16.8 - - + +
394C ALA 2.8 31.2 + - - +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 6.0 2.5 - - + -
206C ILE* 4.5 8.5 - - + -
207C ILE* 1.3 72.3 - - - +
209C ALA* 1.3 62.0 + - - +
216C LYS* 4.9 0.8 - - + +
219C PHE* 3.8 38.1 - - + -
223C ILE* 5.8 0.4 - - + -
358C ILE* 4.4 17.5 - - + -
359C ALA 2.9 6.9 + - - -
360C LEU* 3.3 25.1 - - + +
361C SER 2.8 23.6 + - - +
394C ALA* 3.1 28.3 - - + +
396C LEU* 4.0 18.6 - - + -
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Residues in contact with ALA 209 (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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207C ILE* 4.0 1.7 + - + +
208C VAL* 1.3 75.5 - - - +
210C ALA* 1.3 60.7 + - - +
361C SER* 3.4 25.6 - - - +
363C LEU* 3.9 15.3 - - + -
380C ILE* 4.3 8.7 - - + -
393C VAL* 5.8 0.4 - - + -
394C ALA 2.8 9.6 + - - +
395C PHE* 3.2 30.2 - - + -
396C LEU 3.0 22.9 + - - +
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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