Contacts of the strand formed by residues 207 - 213 (chain C) in PDB entry 3ORH
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 ILE 207 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C PHE* 4.1 25.8 - - + -
194C VAL* 4.6 5.8 - - + -
197C LEU* 3.9 27.6 - - + -
198C LEU* 4.0 20.6 - - + -
202C PHE* 4.5 5.2 - - + -
203C ARG 3.6 16.8 - - - +
204C ARG* 2.9 48.8 + - - +
205C GLU 3.4 1.6 - - - +
206C ASN* 1.4 78.9 - - - +
208C ARG* 1.3 69.8 + - - +
209C THR* 5.0 0.9 - - + -
232C LEU 3.6 2.7 - - - -
233C VAL* 4.1 27.1 - - + -
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Residues in contact with ARG 208 (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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205C GLU 3.4 24.8 + - - +
206C ASN* 3.9 23.4 + - - +
207C ILE* 1.3 77.2 - - - +
209C THR* 1.3 71.5 + - - +
231C PRO* 3.6 0.3 - - - +
232C LEU* 2.8 48.0 + - + +
234C THR* 4.4 11.3 + - - -
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Residues in contact with THR 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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186C THR* 4.3 12.0 - - - +
189C PHE* 3.6 39.0 - - + -
204C ARG* 6.2 1.8 - - - +
207C ILE* 5.0 2.2 - - + -
208C ARG* 1.3 82.6 - - - +
210C GLU* 1.3 62.8 + - - +
211C VAL* 4.1 2.2 + - - +
229C ILE* 3.8 30.0 - - + +
230C THR 3.4 4.5 - - - -
231C PRO* 4.3 4.3 - - + -
232C LEU* 4.6 0.7 - - - -
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Residues in contact with GLU 210 (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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52C ALA* 4.9 10.3 - - + +
56C ALA* 5.7 1.3 - - - +
209C THR* 1.3 74.9 - - - +
211C VAL* 1.3 65.5 + - - +
212C MET* 4.1 1.4 + - + +
228C MET 3.8 0.3 - - - +
229C ILE* 3.4 2.6 - - - -
230C THR* 2.7 54.6 + - - +
232C LEU* 3.7 30.1 - - + +
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Residues in contact with VAL 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ILE* 3.8 20.4 - - + -
186C THR* 3.8 21.1 - - + -
209C THR* 4.1 3.2 + - - +
210C GLU* 1.3 78.1 - - - +
212C MET* 1.3 64.7 + - - +
227C GLN* 3.7 38.8 - - + +
228C MET 3.4 7.6 - - - +
229C ILE* 4.1 9.4 - - + -
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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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48C PRO* 3.7 19.1 - - + +
49C TYR* 3.8 32.1 - - + -
52C ALA* 3.7 25.6 - - + +
210C GLU* 5.4 1.1 - - + +
211C VAL* 1.3 79.0 - - - +
213C ALA* 1.3 65.5 + - - +
214C LEU* 5.0 1.6 - - - -
227C GLN* 3.3 6.2 - - - +
228C MET* 3.0 50.3 + - + +
230C THR* 5.2 2.2 - - - +
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Residues in contact with ALA 213 (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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48C PRO* 6.0 0.5 - - - +
212C MET* 1.3 78.4 - - - +
214C LEU* 1.3 61.7 + - - +
215C VAL* 6.4 0.2 - - + -
226C PRO 3.8 7.9 - - - +
227C GLN* 4.7 5.6 - - + +
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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