Contacts of the strand formed by residues 202 - 207 (chain A) in PDB entry 6S6A
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 GLU 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA 3.2 2.2 - - - -
201A ASP* 1.3 82.7 - - + +
203A VAL* 1.3 70.7 - - - +
204A LEU* 4.2 19.5 - - + +
216A HIS* 3.9 5.0 + - - -
217A TYR* 3.1 12.0 - - - +
218A GLN* 3.5 16.3 - - - +
222A GLN* 3.5 9.6 - - - +
227A ARG* 2.7 46.0 + - - -
273A MET 3.8 1.3 - - - +
275A VAL* 2.8 45.6 + - + +
299C TYR* 2.8 25.6 + - + +
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Residues in contact with VAL 203 (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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191A LEU* 3.5 26.3 - - + +
194A PHE* 4.1 11.4 - - + -
195A ALA* 3.7 31.6 - - + -
198A ILE* 4.9 0.2 - - + -
200A ALA* 3.7 14.1 - - + -
202A GLU* 1.3 77.2 - - - +
204A LEU* 1.3 63.1 + - - +
216A HIS* 3.2 5.4 - - - -
217A TYR 2.9 34.2 + - - +
272A VAL* 3.7 26.7 - - + -
273A MET 3.3 5.4 - - - +
274A VAL* 4.3 10.5 - - + -
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Residues in contact with LEU 204 (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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202A GLU* 4.2 10.1 - - + -
203A VAL* 1.3 75.3 - - - +
205A LEU* 1.3 60.4 + - - +
206A PHE* 3.6 27.8 - - + -
213A VAL* 4.8 3.8 - - + -
215A SER 3.5 4.9 - - - +
216A HIS* 3.9 9.4 - - + -
228A PHE* 3.4 41.3 - - + -
231A ILE* 4.3 11.4 - - + -
272A VAL* 3.3 10.4 - - - +
273A MET* 3.0 54.9 + - + +
299C TYR* 3.6 23.6 - - + +
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Residues in contact with LEU 205 (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* 4.0 28.3 - - + -
191A LEU* 3.9 18.3 - - + +
204A LEU* 1.3 73.0 - - - +
206A PHE* 1.3 62.3 + - - +
213A VAL* 3.5 7.1 - - - +
214A ILE* 3.1 47.2 + - + -
215A SER* 2.8 24.4 + - - +
266A PHE* 3.5 36.3 - - + -
267A THR* 6.4 0.7 - - + -
270A THR* 4.3 10.1 - - + +
271A TYR 3.6 11.2 - - - +
272A VAL* 4.2 6.3 - - + -
297A PHE* 5.1 3.1 - - + -
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Residues in contact with PHE 206 (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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204A LEU* 3.6 39.7 - - + -
205A LEU* 1.3 73.3 - - - +
207A GLU* 1.3 65.0 + - - +
211A PHE* 3.4 52.5 - + + -
212A LEU 3.3 7.6 - - - +
213A VAL* 3.8 24.0 - - + -
214A ILE* 4.2 1.8 - - - -
231A ILE* 3.8 19.3 - - + -
232A SER* 3.8 8.1 - - - -
235A ILE* 4.7 1.6 - - + -
263A ILE* 5.6 0.7 - - + -
270A THR* 3.1 11.0 - - - -
271A TYR* 2.8 49.8 + - + +
272A VAL 4.4 0.7 - - - -
273A MET* 3.8 18.2 - - + -
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Residues in contact with GLU 207 (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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51A ARG 4.1 9.4 - - - +
52A PHE* 3.5 42.0 - - + -
53A LEU* 3.9 22.0 + - + -
206A PHE* 1.3 71.5 - - - +
208A ARG* 1.3 62.1 + - - +
209A ALA* 2.9 30.6 + - - +
210A THR* 2.9 27.7 + - - +
211A PHE* 2.8 31.4 + - - -
212A LEU 3.0 10.4 + - - +
214A ILE* 4.1 5.7 - - + +
269A ASN* 3.8 17.0 - - - +
270A THR* 4.4 2.5 - - - -
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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