Contacts of the strand formed by residues 196 - 201 (chain A) in PDB entry 6EKK
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 ARG 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ARG* 1.3 73.3 - - - +
197A ILE* 1.3 54.7 + - - +
241A ALA 3.5 17.9 - - - -
242A PRO* 2.7 34.8 + - - +
243A MET 3.6 15.0 - - - +
244A PRO* 4.3 2.5 - - + -
245A TYR* 3.6 25.6 - - + +
263A ASP 4.0 4.4 + - - -
264A ASP* 2.8 43.2 + - - +
265A VAL* 3.4 15.4 - - + +
266A VAL* 2.8 33.4 + - - +
279A PHE* 5.6 1.4 - - - -
79C ARG* 3.1 32.2 + - - +
80C GLY* 4.2 6.5 - - - -
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Residues in contact with ILE 197 (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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187A LEU* 3.8 25.1 - - + +
190A SER* 3.6 34.8 - - - +
191A MET* 3.7 30.1 - - + +
195A ARG* 3.9 11.7 - - + +
196A ARG* 1.3 79.4 - - - +
198A LEU* 1.3 62.3 + - - +
199A ILE* 4.3 7.0 - - + -
223A TRP* 4.5 5.2 - - + -
245A TYR* 2.8 20.7 + - - +
246A LEU* 3.5 21.9 - - + -
247A ILE 2.9 27.2 + - - +
266A VAL* 3.4 11.7 - - + +
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Residues in contact with LEU 198 (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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196A ARG 4.2 0.2 + - - -
197A ILE* 1.3 74.5 - - - +
199A ILE* 1.3 62.3 + - - +
200A ILE* 4.1 11.9 - - + -
239A CYS* 4.1 9.6 - - - -
245A TYR* 4.5 4.5 - - + +
247A ILE* 3.4 33.9 - - + +
249A ILE* 3.9 26.2 - - + -
257A VAL* 3.6 31.9 - - + -
262A LEU* 4.3 13.5 - - + -
265A VAL* 4.1 9.2 - - + -
266A VAL 2.7 14.0 + - - +
267A ILE* 3.3 15.6 - - + +
268A LEU 2.9 26.0 + - - +
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Residues in contact with ILE 199 (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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187A LEU* 3.9 32.3 - - + -
197A ILE* 4.3 11.2 - - + -
198A LEU* 1.3 78.5 - - - +
200A ILE* 1.3 63.7 + - - +
207A LEU* 3.3 16.2 - - + +
210A CYS* 4.2 25.4 - - + +
211A ILE* 3.8 28.0 - - + -
214A SER* 4.4 3.8 - - - +
246A LEU* 4.6 3.6 - - + -
247A ILE 2.9 8.1 + - - +
248A GLY* 3.4 0.7 - - - -
249A ILE* 2.9 26.0 + - - +
268A LEU* 3.5 8.3 - - + +
270A VAL* 3.5 27.8 - - + -
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Residues in contact with ILE 200 (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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198A LEU* 4.3 7.4 - - + -
199A ILE* 1.3 78.0 - - - +
201A CYS* 1.3 66.2 + - - +
249A ILE* 3.3 34.1 - - + +
250A HIS 4.3 0.4 - - - +
251A LEU* 3.7 35.4 - - + -
254A MET* 3.8 31.6 - - + -
257A VAL* 5.3 3.4 - - + -
267A ILE* 3.7 25.4 - - + -
268A LEU 2.8 15.9 + - - +
269A ASN* 3.7 8.0 - - + +
270A VAL* 2.8 30.0 + - - +
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Residues in contact with CYS 201 (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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200A ILE* 1.3 77.5 - - - +
202A SER* 1.3 72.7 + - - +
203A LYS* 3.4 28.5 - - - +
206A THR* 3.8 24.9 - - - -
207A LEU* 3.9 18.6 - - + +
249A ILE 3.3 6.7 + - - -
250A HIS* 3.3 10.7 - - - -
251A LEU* 2.8 21.8 + - - -
270A VAL* 3.9 13.9 - - + -
271A ASP* 3.3 16.4 - - - -
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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