Contacts of the strand formed by residues 207 - 211 (chain A) in PDB entry 6B0Z
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 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A SER* 3.8 26.2 - - - +
197A PHE* 3.6 37.9 - - + -
200A ALA* 4.0 13.9 - - + +
206A PRO* 1.3 75.0 - - - +
208A TYR* 1.3 82.9 + - - +
227A PHE* 4.7 2.7 - - + -
239A PHE* 4.4 2.7 - - + -
245A TRP 2.9 11.1 + - - +
246A TYR* 3.2 18.4 - - + -
247A GLU 3.1 23.2 + - - -
266A ILE* 3.6 28.3 - - + +
268A ALA* 4.1 13.9 - - + -
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Residues in contact with TYR 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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206A PRO* 4.4 9.6 - - + -
207A LEU* 1.3 81.2 - - - +
209A LEU* 1.3 55.7 + - - +
245A TRP* 3.1 33.6 + - - -
247A GLU* 3.2 37.9 - - + +
249A ARG* 4.0 14.2 + - + -
254A MET* 3.7 24.9 - - + -
257A GLN* 3.4 28.8 + - - -
265A PHE* 4.0 30.5 - + + -
266A ILE 3.0 15.3 + - - +
267A TRP* 3.5 2.6 - - - -
268A ALA* 2.8 33.4 + - - +
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Residues in contact with LEU 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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192A PHE* 4.3 10.1 - - + -
208A TYR* 1.3 73.2 - - - +
210A SER* 1.3 64.0 + - - +
211A THR* 4.0 14.6 - - + -
223A PHE* 3.8 22.0 - - + +
224A LYS* 4.1 6.1 - - - -
227A PHE* 3.6 32.3 - - + -
246A TYR* 3.4 32.0 - - + +
247A GLU 3.1 6.3 + - - -
248A HIS* 3.3 6.3 - - + -
249A ARG* 2.7 34.3 + - - +
268A ALA* 3.3 25.4 - - + +
270A LYS* 4.4 4.7 - - + -
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Residues in contact with SER 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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208A TYR 4.1 0.2 - - - -
209A LEU* 1.3 72.1 - - - +
211A THR* 1.3 67.5 + - - +
249A ARG 3.0 9.2 - - - -
251A ILE* 3.6 26.1 - - - +
254A MET* 4.1 12.8 - - - -
267A TRP* 2.9 28.9 + - - +
268A ALA 3.0 5.9 + - - -
269A CYS* 3.7 11.8 - - - -
270A LYS* 3.1 23.5 + - - +
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Residues in contact with THR 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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209A LEU* 4.0 15.9 - - + -
210A SER* 1.3 81.0 - - - +
212A LYS* 1.3 59.7 + - - +
213A ASN* 3.3 14.3 + - - +
220A ASP* 3.6 28.5 - - + +
223A PHE* 4.3 2.7 - - + -
224A LYS 4.8 0.2 - - - +
248A HIS* 2.5 35.4 + - + +
249A ARG 3.1 4.6 + - - -
250A LEU* 3.5 6.4 - - - +
251A ILE* 2.8 29.8 + - - +
270A LYS* 4.1 18.8 - - + -
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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