Contacts of the strand formed by residues 207 - 213 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.1 25.8 - - + -
194A VAL* 4.6 7.2 - - + -
197A LEU* 4.0 27.4 - - + -
198A LEU* 4.0 20.9 - - + -
202A PHE* 4.5 4.9 - - + -
203A ARG 3.6 16.2 - - - +
204A ARG* 2.9 46.3 + - - +
205A GLU 4.7 1.4 - - - +
206A ASN* 1.3 80.6 - - - +
208A ARG* 1.3 72.2 + - - +
209A THR* 5.1 0.9 - - + -
232A LEU 3.6 2.2 - - - -
233A VAL* 4.1 26.9 - - + -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL* 5.5 0.8 - - - +
204A ARG* 6.1 0.4 - - - +
205A GLU 4.9 6.3 - - - +
206A ASN* 4.1 7.9 + - - +
207A ILE* 1.3 79.8 - - - +
209A THR* 1.3 72.7 + - - +
231A PRO* 3.7 0.5 - - - +
232A LEU* 2.9 86.0 + - + +
234A THR* 3.2 25.7 + - - -
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A THR* 4.3 11.4 - - - +
189A PHE* 3.6 40.6 - - + -
204A ARG* 6.4 0.2 - - - +
207A ILE* 5.1 0.9 - - + -
208A ARG* 1.3 84.1 - - - +
210A GLU* 1.3 64.5 + - - +
211A VAL* 4.2 2.1 + - - +
229A ILE* 3.7 29.4 - - + +
230A THR 3.4 4.7 - - - -
231A PRO* 4.3 3.8 - - + -
232A LEU* 4.6 1.1 - - - -
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 4.9 9.9 - - - +
56A ALA* 5.6 0.9 - - - +
209A THR* 1.3 75.1 - - - +
211A VAL* 1.3 65.6 + - - +
212A MET* 5.5 0.9 - - + +
228A MET 3.8 0.5 - - - +
229A ILE* 3.4 2.8 - - - -
230A THR* 2.7 54.8 + - - +
232A LEU* 3.7 30.5 - - + +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ILE* 3.8 21.5 - - + -
186A THR* 3.8 20.6 - - + -
209A THR* 4.2 3.1 + - - +
210A GLU* 1.3 78.6 - - - +
212A MET* 1.3 66.0 + - - +
227A GLN* 3.7 38.8 - - + +
228A MET 3.4 7.6 - - - +
229A ILE* 4.1 9.2 - - + -
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Residues in contact with MET 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.7 32.5 - - + +
49A TYR* 3.8 29.2 - - + +
52A ALA* 4.2 14.4 - - + -
210A GLU* 5.5 0.4 - - + +
211A VAL* 1.3 77.2 - - - +
213A ALA* 1.3 78.0 + - - +
214A LEU* 4.1 9.2 - - + -
227A GLN* 3.3 7.5 - - - +
228A MET* 3.0 47.4 + - + +
230A THR* 5.2 2.9 - - - +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A MET* 1.3 83.5 - - - +
214A LEU* 1.3 62.1 + - - +
215A VAL* 6.4 0.7 - - + -
226A PRO 3.8 8.5 - - - +
227A GLN* 4.7 5.4 - - + +
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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