Contacts of the strand formed by residues 211 - 216 (chain C) in PDB entry 4OA5
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 MET 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.7 35.0 - - + -
44C GLU* 4.6 7.4 - - + -
47C MET* 3.8 32.3 - - + -
48C LEU* 4.5 6.3 - - + -
134C PHE* 3.9 15.5 - - + -
160C VAL* 3.9 16.4 - - + -
161C ALA 3.6 21.8 - - - +
162C ASP* 3.7 14.6 - - + +
204C ILE* 3.9 0.9 - - - -
205C ILE* 2.8 43.1 + - + +
207C THR* 3.6 6.8 + - + +
210C GLY* 1.3 70.9 - - - +
212C MET* 1.3 64.1 + - - +
213C VAL* 3.5 6.2 + - + -
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Residues in contact with MET 212 (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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17B PHE* 3.7 17.3 - - + -
159C ILE 4.2 7.2 - - - +
160C VAL* 3.2 12.5 - - - +
161C ALA* 2.8 40.8 + - + +
164C THR* 3.6 17.1 + - + +
190C PHE* 4.2 4.3 - - + -
191C ASN* 3.5 24.9 - - - +
194C LEU* 3.7 34.1 - - + -
202C SER* 4.0 19.3 - - - -
203C THR 3.7 11.4 - - - +
204C ILE* 3.6 19.1 - - + +
210C GLY 3.6 2.6 + - - -
211C MET* 1.3 70.1 - - - +
213C VAL* 1.3 66.5 + - - +
214C SER* 4.5 0.2 - - - -
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Residues in contact with VAL 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 12.9 - - + +
54B MET* 3.8 29.6 - - + -
47C MET* 5.8 0.2 - - + -
51C LEU* 3.7 34.1 - - + -
158C LEU* 5.0 5.2 - - + -
159C ILE 3.6 2.7 - - - -
160C VAL* 4.4 11.2 - - + -
202C SER* 3.4 1.7 - - - -
203C THR* 2.9 35.7 + - + +
205C ILE* 4.0 15.9 - - + -
211C MET* 3.9 12.6 - - + +
212C MET* 1.3 78.9 - - - +
214C SER* 1.3 62.6 + - - +
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Residues in contact with SER 214 (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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50B LEU* 4.9 0.7 - - - -
158C LEU* 3.3 8.6 - - - +
159C ILE* 2.8 45.7 + - - -
160C VAL* 5.1 0.2 - - - +
194C LEU* 3.7 18.8 - - - +
200C TYR* 3.3 17.5 - - - +
201C LEU 3.4 3.6 - - - -
202C SER* 2.7 26.6 + - - -
212C MET* 4.5 5.4 - - - -
213C VAL* 1.3 76.4 - - - +
215C ILE* 1.3 64.1 + - - +
216C LYS 3.9 0.3 + - - -
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Residues in contact with ILE 215 (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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50B LEU* 3.4 26.7 - - + +
53B ARG* 3.6 32.5 - - + -
54B MET* 3.7 18.2 - - + +
304B IOD 4.0 13.7 - - + -
156C GLY* 3.9 22.0 - - - +
157C GLY 3.5 2.9 - - - -
158C LEU* 3.8 15.9 - - + -
200C TYR* 3.2 6.8 - - - -
201C LEU* 2.9 37.5 + - + +
214C SER* 1.3 74.1 - - - +
216C LYS* 1.3 72.9 + - - +
217C LEU* 3.4 4.8 + - + +
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Residues in contact with LYS 216 (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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149C ALA 3.4 12.6 - - - +
150C LYS* 3.3 32.5 + - - +
153C ILE* 2.8 36.5 + - + +
154C ARG 3.7 11.2 - - - +
155C LYS 4.0 0.8 - - - +
156C GLY* 2.7 33.4 + - - -
157C GLY 2.9 17.5 + - - +
159C ILE* 4.4 19.3 - - + -
199C LYS 3.9 4.5 - - - +
200C TYR* 4.0 11.9 - - + -
214C SER* 3.9 0.8 + - - -
215C ILE* 1.3 72.9 - - - +
217C LEU* 1.3 56.6 + - - +
218C THR* 2.8 35.9 + - - +
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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