Contacts of the strand formed by residues 213 - 218 (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 VAL 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.4 28.7 + - - +
177A VAL* 6.1 0.3 - - - +
178A TYR* 5.2 1.0 + - - +
204A LEU* 4.8 5.8 - - + -
205A LEU 3.5 8.1 - - - +
206A PHE* 3.8 14.1 - - + -
212A LEU* 1.3 71.8 - - - +
214A ILE* 1.3 63.0 + - - +
215A SER 3.7 19.1 - - - +
216A HIS* 4.5 6.7 - - + -
228A PHE* 3.6 37.5 - - + +
232A SER* 3.3 19.3 - - - +
403A 9JE 3.9 27.4 - - - +
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Residues in contact with ILE 214 (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 PHE* 4.1 21.3 - - + -
53A LEU* 3.9 21.1 - - + -
177A VAL* 5.2 1.3 - - + -
178A TYR* 3.4 23.9 - - - -
181A ILE* 3.8 25.6 - - + -
184A VAL* 4.0 6.8 - - - +
187A LEU* 4.4 6.7 - - + +
205A LEU* 3.1 40.1 + - + +
207A GLU 4.1 7.2 - - - +
212A LEU* 3.6 11.4 - - + +
213A VAL* 1.3 75.9 - - - +
215A SER* 1.3 68.4 + - - +
270A THR* 3.8 19.7 - - + -
403A 9JE 4.3 0.4 - - - -
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL 4.6 0.3 + - - -
187A LEU* 3.6 21.0 - - - +
188A GLU* 3.6 27.9 - - - +
191A LEU* 3.9 12.1 - - - -
204A LEU* 3.5 1.0 - - - -
205A LEU* 2.8 46.6 + - - +
213A VAL* 3.7 7.1 - - - +
214A ILE* 1.3 86.0 + - - +
216A HIS* 1.3 63.6 + - - +
403A 9JE 4.0 2.3 - - - -
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 3.7 11.7 + - - +
191A LEU* 3.8 5.0 - - - +
192A ARG* 2.8 26.5 + - - -
202A GLU* 3.9 2.6 + - - -
203A VAL 3.2 7.6 - - - -
204A LEU* 3.9 18.4 - - + -
213A VAL* 4.5 2.0 - - + -
215A SER* 1.3 77.9 - - - +
217A TYR* 1.3 59.8 + - - +
218A GLN* 3.1 38.0 + - + -
228A PHE* 3.6 32.3 - + + -
403A 9JE 3.4 23.3 - - + +
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Residues in contact with TYR 217 (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* 4.6 4.5 - - + +
192A ARG* 3.5 40.6 - - + +
195A ALA* 3.3 32.1 - - + -
196A GLN* 4.1 34.2 + - + +
200A ALA 3.4 25.5 + - - -
201A ASP 4.1 2.7 - - - -
202A GLU* 3.1 14.1 - - - +
203A VAL* 2.9 33.8 + - + +
216A HIS* 1.3 77.8 + - - +
218A GLN* 1.3 83.9 + - - +
219A CYS* 4.0 13.7 - - + +
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Residues in contact with GLN 218 (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 ARG* 5.1 0.2 - - - +
201A ASP 3.5 7.9 - - - -
202A GLU* 3.5 11.4 - - - +
216A HIS* 3.1 21.6 - - + -
217A TYR* 1.3 97.9 - - - +
219A CYS* 1.3 67.9 + - - +
220A LYS 4.9 0.9 - - - +
221A GLU* 3.4 37.8 + - - +
222A GLN* 4.2 10.1 - - - +
227A ARG* 2.8 28.4 + - - -
228A PHE* 4.1 0.9 - - - -
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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