Contacts of the helix formed by residues 191 - 202 (chain D) in PDB entry 4IRV
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 PHE 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.5 24.0 - - + -
74D SER* 3.7 23.6 - - - -
77D ALA* 3.8 17.7 - - + -
84D LYS* 3.5 28.9 - - + -
87D TYR* 4.3 2.5 - - + -
88D PHE* 3.7 40.8 - + + -
91D PHE* 5.5 0.7 - - + -
187D PHE* 3.1 47.5 + + - +
190D VAL* 1.3 85.5 - - + +
192D ASP* 1.3 57.0 + - - +
193D GLU* 3.1 4.7 + - - -
194D SER* 3.1 7.7 + - - +
195D LEU* 2.8 40.3 + - + +
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Residues in contact with ASP 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D MSE 3.3 19.1 + - - +
189D GLY* 3.4 13.0 + - - +
190D VAL 3.4 3.2 + - - -
191D PHE* 1.3 77.5 - - - +
193D GLU* 1.3 63.8 + - + +
195D LEU* 3.9 4.2 - - - +
196D LYS* 2.9 64.2 + - - +
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Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LYS* 6.1 7.9 - - + +
190D VAL 6.1 0.7 - - - +
191D PHE 3.1 0.8 - - - -
192D ASP* 1.3 81.4 - - + +
194D SER* 1.3 67.7 + - - +
196D LYS* 3.5 3.8 + - - +
197D GLU* 3.2 22.7 + - - +
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Residues in contact with SER 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LYS* 5.5 2.9 + - - +
85D ASN* 4.3 13.7 + - - -
88D PHE* 3.5 43.9 - - - +
191D PHE* 3.1 11.1 + - - -
193D GLU* 1.3 78.7 - - - +
195D LEU* 1.3 57.8 + - - +
197D GLU* 3.4 15.2 + - - +
198D ARG* 3.0 31.2 + - - +
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 4.2 8.7 - - + -
187D PHE* 4.0 17.7 - - + +
188D MSE 3.9 34.8 - - + +
191D PHE* 2.8 37.9 + - + +
192D ASP* 3.9 4.3 - - - +
194D SER* 1.3 74.6 - - - +
196D LYS* 1.3 66.3 + - - +
198D ARG* 3.1 9.8 + - + +
199D GLN* 2.9 24.6 + - - +
213D LEU* 4.2 20.0 - - + -
217D LEU* 3.6 30.5 - - + -
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ASP* 2.9 48.4 + - - +
193D GLU* 4.1 4.5 - - - +
195D LEU* 1.3 74.1 - - - +
197D GLU* 1.3 64.0 + - - +
199D GLN* 3.2 20.3 + - - +
200D GLU* 3.0 27.5 + - - +
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Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 5.7 0.3 - - - -
193D GLU 3.2 15.8 + - - +
194D SER* 3.4 21.3 - - - +
195D LEU 3.1 0.4 - - - -
196D LYS* 1.3 78.5 - - - +
198D ARG* 1.3 68.3 + - - +
200D GLU* 3.4 13.6 + - - +
201D ALA* 3.2 19.4 + - - +
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Residues in contact with ARG 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D PHE* 3.5 26.8 - - - -
92D ILE* 4.0 22.7 - - - +
194D SER 3.0 17.0 + - - +
195D LEU* 3.1 10.7 + - + +
197D GLU* 1.3 81.5 + - - +
199D GLN* 1.3 61.0 + - - +
201D ALA* 3.3 9.8 + - - +
202D GLU* 3.2 25.3 + - - +
211D ASP* 2.7 32.1 + - - +
213D LEU* 4.5 5.6 - - - -
214D ASP* 2.9 38.4 + - - +
217D LEU* 6.4 1.1 - - + -
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Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU 2.9 14.7 + - - +
196D LYS* 3.7 23.3 - - - +
198D ARG* 1.3 74.1 - - - +
200D GLU* 1.3 67.9 + - - +
202D GLU* 3.5 19.9 + - + +
203D LYS* 4.8 1.4 - - - +
220D ILE* 5.7 10.5 - - + +
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D LYS 3.0 14.8 + - - +
197D GLU* 3.6 15.0 - - - +
198D ARG 3.3 0.2 - - - -
199D GLN* 1.3 79.0 - - - +
201D ALA* 1.3 63.6 + - - +
203D LYS* 3.0 58.6 + - - +
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ASN* 5.4 11.0 - - - +
197D GLU 3.2 10.3 + - - +
198D ARG* 3.5 13.0 - - - +
199D GLN 3.3 0.2 - - - -
200D GLU* 1.3 78.6 - - - +
202D GLU* 1.3 58.4 + - + +
203D LYS 2.7 9.1 + - - +
205D GLY* 3.1 20.7 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D ARG 3.2 13.2 + - - +
199D GLN* 3.9 12.5 - - + +
200D GLU 3.1 2.5 + - - -
201D ALA* 1.3 74.0 - - + +
203D LYS* 1.3 58.0 + - - +
205D GLY 4.3 1.1 - - - -
206D GLY* 3.1 32.9 - - - +
207D PRO* 3.9 0.9 - - - +
208D THR* 2.9 28.2 - - + +
214D ASP* 4.1 21.1 - - + +
218D SER* 3.9 22.0 - - - -
755H GLN* 3.8 15.6 + - - -
759H ILE* 5.4 1.0 - - - +
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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