Contacts of the strand formed by residues 214 - 220 (chain A) in PDB entry 3SRG
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.0 9.4 - - - -
206A THR* 3.4 2.6 - - - -
207A TYR* 2.8 48.9 + - + +
212A ASP* 2.6 36.1 + - - +
213A VAL* 1.4 75.8 - - - +
215A VAL* 1.3 70.6 + - - +
216A VAL* 3.5 10.4 + - + +
253A ASN* 3.1 28.7 + - - +
254A TRP* 4.1 14.1 + - - +
255A THR* 3.4 29.2 - - - +
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Residues in contact with VAL 215 (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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163A LEU* 3.8 29.3 - - + +
204A PHE* 3.8 22.7 - - + -
205A VAL 3.5 6.3 - - - +
206A THR* 4.4 1.3 - - - +
214A ARG* 1.3 79.7 - - - +
216A VAL* 1.4 65.9 + - - +
217A ALA* 3.6 22.7 - - - +
218A GLU* 4.1 22.2 - - + +
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Residues in contact with VAL 216 (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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179A TYR* 3.9 10.3 - - + -
205A VAL* 2.7 35.1 + - + +
207A TYR* 3.8 24.7 - - + +
214A ARG* 3.5 11.9 + - + +
215A VAL* 1.4 78.6 - - - +
217A ALA* 1.3 64.7 + - - +
248A TYR* 5.0 1.0 - - - -
254A TRP 4.1 14.8 - - - +
255A THR* 4.7 8.3 - - + -
256A LEU* 3.6 46.5 + - + +
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Residues in contact with ALA 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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204A PHE* 3.4 2.1 - - - +
205A VAL* 2.8 37.2 + - + +
215A VAL* 3.6 3.7 - - - +
216A VAL* 1.3 83.4 - - + +
218A GLU* 1.3 64.6 + - - +
220A PHE* 3.8 13.2 - - + -
237A ILE* 4.7 3.6 - - + -
248A TYR* 3.7 34.8 - - + +
256A LEU* 5.0 0.7 - - + -
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Residues in contact with GLU 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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202A TRP 5.8 0.2 - - - +
203A SER 3.8 1.3 - - - -
204A PHE* 3.8 16.6 - - + -
215A VAL* 4.1 14.9 - - + +
217A ALA* 1.3 79.9 - - - +
219A GLY* 1.3 65.4 + - - +
220A PHE* 3.6 7.6 - - - -
248A TYR* 5.4 0.4 + - - -
1363A CA 3.6 14.2 - - - -
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Residues in contact with GLY 219 (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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201A ALA* 3.2 29.4 - - - +
202A TRP* 4.7 2.9 - - - -
203A SER 3.0 6.8 + - - -
218A GLU* 1.3 78.3 - - - +
220A PHE* 1.3 58.9 + - - +
221A ASP 4.1 0.3 + - - -
239A GLU* 4.2 3.6 - - - +
356A LMT 5.9 3.8 - - - -
1363A CA 4.1 8.8 - - - -
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Residues in contact with PHE 220 (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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201A ALA* 3.0 21.0 - - - -
203A SER* 3.0 40.3 + - - +
204A PHE* 4.1 6.1 - - - -
205A VAL* 3.9 7.9 - - + -
217A ALA* 3.8 12.1 - - + -
218A GLU* 3.7 27.1 - - - -
219A GLY* 1.3 78.2 - - - +
221A ASP* 1.3 60.5 + - - +
222A PHE 3.4 0.2 + - - -
223A ALA* 3.9 16.8 - - + +
237A ILE* 4.0 21.3 - - + -
239A GLU* 3.4 24.0 - - + +
246A HIS* 3.8 30.3 - + - -
248A TYR* 3.7 20.2 - - - -
1363A CA 4.3 5.6 - - - -
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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