Contacts of the helix formed by residues 218 - 227 (chain A) in PDB entry 2V5E
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 ASP 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLY 5.1 6.6 - - - +
152A ASN* 4.7 4.4 + - - +
217A ARG* 1.3 84.2 - - - +
219A ILE* 1.3 61.8 + - + +
220A ALA* 3.2 14.5 + - - +
221A CYS* 2.9 33.7 + - - +
222A THR* 3.2 19.7 + - - +
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Residues in contact with ILE 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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218A ASP* 1.3 74.1 - - + +
220A ALA* 1.3 66.7 + - - +
222A THR* 3.5 11.4 - - - +
223A GLU* 3.1 41.1 + - + +
304A SER* 4.4 19.1 - - - +
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Residues in contact with ALA 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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152A ASN* 4.3 8.5 + - - +
218A ASP* 3.2 12.2 + - - +
219A ILE* 1.3 84.3 - - + +
221A CYS* 1.3 60.7 + - - +
223A GLU* 4.4 3.2 - - - +
224A ARG* 3.5 20.4 + - - +
118B LEU* 5.4 2.4 - - - +
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Residues in contact with CYS 221 (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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152A ASN* 3.7 33.8 - - + +
154A CYS* 3.4 17.6 - - - -
215A SER 3.7 5.2 - - - -
216A CYS* 2.1 55.4 - - + -
217A ARG 4.6 0.9 - - - +
218A ASP* 2.9 22.2 + - - +
220A ALA* 1.3 76.7 - - - +
222A THR* 1.3 58.6 + - - +
224A ARG* 3.2 6.4 + - - +
225A ARG* 2.9 24.4 + - - +
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Residues in contact with THR 222 (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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216A CYS* 3.4 24.7 - - + +
217A ARG 5.7 0.2 - - - -
218A ASP 3.2 14.8 + - - +
219A ILE* 3.5 20.4 + - - +
221A CYS* 1.3 75.3 - - - +
223A GLU* 1.3 60.8 + - - +
225A ARG* 3.7 23.3 + - - +
226A ARG* 3.0 28.2 + - - +
301A TYR* 5.9 0.5 - - - +
304A SER* 3.7 31.2 + - - +
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Residues in contact with GLU 223 (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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219A ILE* 3.1 37.9 + - + +
220A ALA* 4.4 3.6 - - - +
222A THR* 1.3 77.8 + - - +
224A ARG* 1.3 63.8 + - - +
226A ARG* 3.1 43.2 + - - +
227A GLN* 3.2 28.1 + - - +
304A SER* 4.3 16.1 - - - -
118B LEU* 3.9 29.3 - - + +
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Residues in contact with ARG 224 (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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152A ASN* 4.3 3.8 - - - +
154A CYS* 3.8 24.2 - - + -
155A LEU* 3.3 40.4 - - - +
158A ALA* 3.7 14.1 - - - +
171A ARG* 4.1 3.0 - - - +
211A MET* 5.4 2.4 - - + +
220A ALA 3.5 13.9 + - - +
221A CYS* 3.2 8.0 + - - +
223A GLU* 1.3 77.9 - - - +
225A ARG* 1.3 63.1 + - - +
227A GLN* 3.1 13.7 + - - +
228A THR* 3.4 12.2 + - - +
59B THR* 4.7 0.8 + - - -
60B LYS* 5.3 2.2 - - - +
61B GLU* 3.0 28.3 + - - +
114B LEU* 2.9 56.2 + - + +
115B ASP 4.8 2.6 + - - -
118B LEU* 4.3 3.7 - - + +
120B TYR* 5.1 0.5 + - - -
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Residues in contact with ARG 225 (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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154A CYS* 3.9 10.3 - - - -
211A MET 4.0 8.7 - - - +
212A LEU* 3.6 26.2 - - - +
213A PHE 5.2 0.2 + - - -
214A CYS* 2.9 32.4 + - - -
215A SER* 4.3 1.0 - - - +
216A CYS* 3.8 21.3 - - - +
221A CYS 2.9 14.8 + - - +
222A THR* 3.7 25.9 + - - +
224A ARG* 1.3 78.4 - - - +
226A ARG* 1.3 60.2 + - - +
228A THR* 3.0 25.9 + - - -
229A ILE 4.9 0.2 + - - -
300A ASN* 4.9 1.6 - - - +
301A TYR* 3.7 32.8 + - + +
304A SER* 5.5 1.2 + - - +
306A SER 3.9 19.0 + - - -
307A LEU* 3.7 25.7 - - - +
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Residues in contact with ARG 226 (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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222A THR 3.0 18.3 + - - +
223A GLU* 3.1 39.9 + - - +
224A ARG 3.3 0.2 - - - -
225A ARG* 1.3 75.6 - - - +
227A GLN* 1.3 85.2 + - - +
228A THR 3.6 0.3 + - - -
229A ILE 4.5 0.9 + - - -
231A PRO* 3.3 22.2 - - - +
235A TYR* 6.2 0.4 - - - -
236A GLU* 4.3 13.1 + - - -
300A ASN* 3.1 41.2 + - - +
301A TYR* 3.8 29.6 - - + +
302A VAL 5.1 6.7 - - - -
304A SER* 5.9 5.2 - - - +
118B LEU* 5.6 0.8 - - - +
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Residues in contact with GLN 227 (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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223A GLU* 3.2 12.8 + - - +
224A ARG 3.1 10.5 + - - +
226A ARG* 1.3 112.9 - - - +
228A THR* 1.3 62.5 + - - +
229A ILE 3.2 3.8 - - - -
230A VAL* 2.9 17.9 + - - +
231A PRO* 3.5 19.6 - - - +
232A VAL* 4.8 12.0 - - - +
114B LEU* 4.2 19.1 - - + -
118B LEU* 4.4 28.5 - - + +
120B TYR* 2.8 22.8 + - + +
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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