Contacts of the helix formed by residues 204 - 214 (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 PRO 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 5.5 0.9 - - - +
166A THR* 4.4 13.2 - - + -
202A LYS 3.8 6.7 - - - +
203A VAL* 1.3 93.7 - - + +
205A ALA* 1.3 66.4 + - - +
206A LYS* 4.6 19.3 - - + +
207A HIS* 3.1 20.7 + - + +
208A SER 3.1 7.8 + - - -
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Residues in contact with ALA 205 (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 VAL 3.4 1.6 + - - -
204A PRO* 1.3 71.5 - - - +
206A LYS* 1.3 57.8 + - - +
208A SER* 3.4 9.4 - - - -
209A TYR* 2.7 67.9 + - + +
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Residues in contact with LYS 206 (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 PRO* 4.6 13.7 - - + +
205A ALA* 1.3 77.8 - - - +
207A HIS* 1.3 93.0 + - + +
210A GLY* 3.7 14.7 + - - -
345A PHE* 4.3 12.0 - - - -
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Residues in contact with HIS 207 (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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157A ALA* 5.2 3.1 - - - +
160A ALA* 4.1 35.6 + - + +
161A CYS* 4.4 1.8 - - + -
164A ASP* 3.8 33.6 + - + +
167A CYS* 3.8 24.9 - - + -
203A VAL* 3.9 5.9 - - + +
204A PRO* 3.1 16.8 + - + +
206A LYS* 1.3 110.5 + - + +
208A SER* 1.3 64.9 + - - +
209A TYR 3.3 0.4 - - - -
210A GLY* 3.3 9.7 + - - -
211A MET* 3.6 16.6 + - - +
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Residues in contact with SER 208 (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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199A PHE* 3.6 33.7 - - - -
200A PHE* 3.7 28.8 + - - -
203A VAL* 3.4 17.8 + - - +
204A PRO 3.1 15.6 + - - -
205A ALA* 3.4 8.1 - - - -
207A HIS* 1.3 77.6 - - - +
209A TYR* 1.3 69.9 + - - +
211A MET* 3.7 4.7 + - - +
212A LEU 3.5 13.3 + - - -
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Residues in contact with TYR 209 (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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200A PHE* 4.9 5.2 - + + -
205A ALA* 2.7 46.5 + - + +
208A SER* 1.3 77.4 - - - +
210A GLY* 1.3 57.5 + - - +
211A MET 3.1 2.7 - - - -
212A LEU* 4.4 1.1 - - - +
213A PHE* 2.7 56.1 + + + +
283A ALA* 4.3 4.5 + - - -
286A LEU* 3.8 23.6 - - + -
287A LEU* 3.2 37.8 + - - +
290A SER* 3.5 23.9 + - - -
345A PHE* 3.4 29.5 - + + -
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Residues in contact with GLY 210 (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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157A ALA* 3.3 18.9 - - - +
206A LYS 3.7 8.2 + - - -
207A HIS 3.3 8.4 + - - -
209A TYR* 1.3 77.3 - - - +
211A MET* 1.3 57.9 + - - +
214A CYS* 3.0 31.7 + - - +
345A PHE* 3.4 19.6 - - - -
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Residues in contact with MET 211 (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* 5.2 2.9 - - - +
157A ALA* 3.9 20.0 - - + +
158A ALA* 3.9 13.9 - - + -
161A CYS* 3.9 29.4 - - - -
171A ARG* 3.6 38.6 - - + +
174A TYR* 5.3 3.1 - - - +
199A PHE* 4.7 12.1 - - + -
207A HIS 3.6 12.4 + - - +
208A SER* 3.7 6.3 + - - +
209A TYR 3.1 0.4 - - - -
210A GLY* 1.3 77.0 - - - +
212A LEU* 1.3 61.7 + - - +
213A PHE 3.5 0.2 - - - -
214A CYS* 3.4 15.5 - - - -
224A ARG* 5.4 2.5 - - + +
225A ARG* 4.0 3.3 - - - +
228A THR* 3.1 38.3 + - + +
120B TYR* 5.9 2.0 - - - +
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Residues in contact with LEU 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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200A PHE* 3.7 19.7 - - + -
208A SER 3.5 13.9 + - - +
209A TYR* 3.2 3.2 + - - +
211A MET* 1.3 79.8 - - - +
213A PHE* 1.3 87.9 + - + +
214A CYS 3.6 0.4 - - - -
225A ARG* 3.6 5.6 - - - +
228A THR* 4.4 10.3 - - + -
229A ILE* 4.2 16.6 - - + -
289A TYR* 4.8 4.9 - - + -
290A SER* 3.9 6.1 - - - -
293A ILE* 3.4 34.5 - - + -
300A ASN* 5.3 3.1 - - - +
301A TYR* 2.7 45.5 + - + -
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Residues in contact with PHE 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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209A TYR* 2.7 57.8 + + + +
212A LEU* 1.3 103.1 - - + +
214A CYS* 1.3 65.5 + - - +
215A SER* 3.5 1.4 + - - -
286A LEU* 4.1 34.3 - - + -
289A TYR* 3.7 30.5 - + - -
290A SER* 4.4 0.7 - - - -
301A TYR* 3.5 16.4 - - - -
342A ILE* 3.6 45.4 - - + +
345A PHE* 3.6 22.8 - + + -
346A GLY* 4.2 2.4 - - - -
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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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153A ASN* 3.9 8.3 - - + +
154A CYS* 2.0 60.1 - - - +
210A GLY 3.0 23.2 + - - +
211A MET* 3.4 17.0 - - - -
212A LEU 3.6 0.4 - - - -
213A PHE* 1.3 78.6 - - - +
215A SER* 1.3 60.7 + - - +
225A ARG* 2.9 32.6 + - - -
345A PHE* 5.1 4.0 - - - -
346A GLY* 5.2 1.3 - - - -
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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