Contacts of the strand formed by residues 211 - 217 (chain A) in PDB entry 5V5W
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 SER 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ARG* 3.6 26.9 - - - +
172A GLY 4.6 0.9 + - - -
210A ALA* 1.3 81.7 - - - +
212A TYR* 1.3 62.7 + - - +
213A THR* 5.3 0.7 - - - -
230A THR* 3.8 11.0 - - - -
231A PHE 3.4 5.4 - - - -
232A ARG* 3.7 13.1 - - - +
303A SO4 3.0 38.1 + - - -
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Residues in contact with TYR 212 (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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134A LEU* 4.7 1.2 - - - +
155A LEU* 3.8 24.9 - - + -
169A TRP* 5.1 7.0 - + + -
170A LYS 3.3 13.7 - - - +
171A ARG* 3.1 47.0 + - + -
175A THR* 5.6 4.3 - - + -
199A LEU* 4.7 10.5 - - + -
201A LEU* 3.5 30.8 - - + +
208A ASP* 3.4 16.2 + - - +
210A ALA 3.5 25.4 - - - -
211A SER* 1.3 73.8 - - - +
213A THR* 1.3 61.4 + - - +
214A CYS 4.4 0.2 + - - -
229A ILE 4.0 0.3 - - - +
230A THR* 3.3 2.8 - - - -
231A PHE* 2.7 35.7 + - - +
233A LEU* 3.8 26.9 - - + +
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Residues in contact with THR 213 (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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168A ILE 3.5 1.4 - - - +
169A TRP* 3.2 14.5 - - - -
170A LYS* 2.8 52.7 + - + -
172A GLY 5.7 1.4 + - - -
211A SER* 5.3 0.9 - - - -
212A TYR* 1.3 75.1 - - - +
214A CYS* 1.3 74.4 + - - +
215A GLN* 3.8 8.1 - - + +
228A ALA* 3.9 16.2 - - + -
229A ILE 3.4 7.6 - - - +
230A THR* 2.9 23.8 + - - +
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Residues in contact with CYS 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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132A PRO* 4.3 1.4 - - - +
134A LEU* 4.8 2.2 - - + +
157A CYS* 2.0 53.8 - - + -
167A PHE* 3.7 18.4 - - - -
168A ILE 3.6 3.6 - - - -
169A TRP* 3.9 18.5 - - + -
212A TYR 4.4 0.2 + - - -
213A THR* 1.3 72.1 - - - +
215A GLN* 1.3 61.2 + - - +
216A VAL* 4.0 6.4 + - - -
227A LYS 4.1 0.2 - - - +
228A ALA* 3.2 2.4 - - - -
229A ILE* 2.8 45.9 + - + +
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Residues in contact with GLN 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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166A ARG 3.6 0.9 - - - +
167A PHE* 3.6 2.1 - - - -
168A ILE* 2.7 64.0 + - + +
170A LYS* 3.0 33.2 + - - +
213A THR* 3.8 6.2 - - + -
214A CYS* 1.3 73.3 - - - +
216A VAL* 1.3 64.3 + - - +
226A ASP* 2.7 37.4 + - + +
227A LYS 3.4 10.5 - - - +
228A ALA* 4.1 12.2 - - + +
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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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129A LEU* 3.6 27.1 - - + +
132A PRO* 3.9 32.8 - - + -
159A VAL* 4.1 11.2 - - + -
165A ALA* 4.6 1.8 - - + -
166A ARG 3.3 4.5 - - - +
167A PHE* 3.9 31.4 - - + -
214A CYS* 4.0 4.3 - - - -
215A GLN* 1.3 76.6 - - - +
217A SER* 1.3 60.8 + - - +
226A ASP* 3.4 6.8 - - - +
227A LYS* 2.8 46.5 + - + +
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Residues in contact with SER 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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129A LEU* 4.0 4.0 - - - -
165A ALA* 3.1 5.4 - - - -
166A ARG* 2.6 54.4 + - - +
168A ILE* 4.8 9.0 - - - -
216A VAL* 1.3 75.0 - - - +
218A VAL* 1.3 59.3 + - - +
219A ARG* 2.7 30.2 + - - +
220A ASN* 4.9 0.9 + - - -
226A ASP* 2.8 29.3 + - - -
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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