Contacts of the helix formed by residues 218 - 224 (chain A) in PDB entry 2V62
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A PHE 3.7 0.8 + - - -
217A THR* 1.3 80.6 + - - +
219A LEU* 1.3 64.9 + - - +
220A ASP* 3.7 3.5 + - - -
221A ALA* 3.0 25.1 + - - +
222A HIS* 3.0 21.8 + - - -
227A LEU* 3.9 2.6 - - - +
231A SER* 3.3 45.3 - - - -
234A GLU* 3.5 13.5 - - - -
235A ILE* 4.0 7.6 - - - +
238A TYR* 4.6 0.4 - - - -
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Residues in contact with LEU 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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217A THR 3.8 0.2 + - - -
218A SER* 1.3 68.0 - - - +
220A ASP* 1.3 65.7 + - - +
222A HIS* 3.2 8.5 + - + +
223A LYS* 2.9 30.9 + - + +
234A GLU* 2.8 16.9 + - - +
238A TYR* 4.0 2.9 - - - +
261A GLN* 3.5 28.0 - - + +
264A LYS* 3.7 14.1 - - + -
265A THR* 3.5 27.6 - - - +
268A LEU* 3.6 30.5 - - + -
281B SER* 3.9 19.5 - - - +
282B GLY* 3.8 23.8 - - - -
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Residues in contact with ASP 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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202A TYR* 4.0 0.3 - - - -
218A SER* 3.2 8.2 + - - +
219A LEU* 1.3 76.0 - - - +
221A ALA* 1.3 62.2 + - - +
223A LYS* 2.9 30.1 + - - +
224A GLY 3.1 3.5 + - - -
225A VAL* 2.9 54.9 + - + +
226A ALA 4.8 3.6 - - - +
227A LEU* 5.0 1.3 - - + -
228A SER* 4.5 0.9 + - - -
230A ARG* 2.8 44.5 + - - +
231A SER* 4.5 11.3 - - - -
234A GLU* 5.4 0.6 - - - +
300A TYR* 4.1 6.2 - - - -
281B SER* 4.3 4.9 - - - -
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Residues in contact with ALA 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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208A LYS 4.1 1.4 - - - +
209A GLY 3.8 0.3 - - - -
210A HIS* 2.9 20.6 + - - -
211A ASN* 3.7 13.5 + - + +
217A THR* 3.2 27.6 - - - +
218A SER* 3.0 18.2 + - - +
220A ASP* 1.3 75.7 - - - +
222A HIS* 1.3 60.7 + - - +
224A GLY* 3.1 12.5 + - - -
225A VAL 4.4 2.5 - - - -
227A LEU* 3.7 20.1 - - + +
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Residues in contact with HIS 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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209A GLY* 3.7 2.3 - - - -
210A HIS* 3.0 51.1 + - - +
214A ILE* 4.4 9.6 - - + -
217A THR* 3.5 18.1 - - + +
218A SER 3.0 23.5 + - - -
219A LEU* 3.4 10.8 - - - +
221A ALA* 1.3 75.7 - - - +
223A LYS* 1.3 58.3 + - - +
224A GLY 3.5 0.7 + - - -
257A PRO 3.4 20.8 + - - -
260A VAL* 3.7 14.0 - - + +
261A GLN* 3.6 34.2 + - + +
264A LYS* 3.0 36.0 + - + +
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Residues in contact with LYS 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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202A TYR* 3.1 19.3 + - - -
204A GLU* 3.6 28.7 - - + +
205A ASN 3.1 22.5 + - - +
206A PRO* 4.4 2.3 - - - +
209A GLY* 4.7 0.7 - - - -
219A LEU* 2.9 21.9 + - + +
220A ASP* 2.9 32.6 + - - +
221A ALA 3.2 0.2 - - - -
222A HIS* 1.3 76.0 - - - +
224A GLY* 1.3 56.9 + - - +
225A VAL* 3.2 7.6 + - + -
230A ARG* 4.2 0.8 - - - +
261A GLN* 3.7 21.5 - - - +
280B PRO 4.7 1.6 + - - -
281B SER* 2.9 31.4 + - - +
284B SER* 5.0 8.4 - - - +
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Residues in contact with GLY 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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203A GLN 3.5 8.3 - - - +
205A ASN* 3.3 30.5 + - - +
208A LYS* 3.5 26.7 - - - +
209A GLY* 4.0 0.2 - - - -
221A ALA* 3.1 10.8 + - - -
222A HIS 3.4 1.4 + - - -
223A LYS* 1.3 78.2 - - - +
225A VAL* 1.3 63.2 + - - +
226A ALA 3.8 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