Contacts of the helix formed by residues 202 - 211 (chain D) in PDB entry 3GV5
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 ASN 202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D ARG* 3.5 7.4 - - - +
30D ILE* 3.8 11.7 - - - -
200D ALA* 3.2 1.2 - - - +
201D SER* 1.3 85.8 + - - +
203D LYS* 1.3 58.5 + - - +
204D LEU* 3.1 13.1 - - - +
205D LEU* 2.8 35.6 - - - +
206D ALA* 3.0 29.6 + - - +
287D GLY 3.0 20.8 - - - +
288D GLU* 4.0 1.2 - - - -
289D ASP* 3.2 34.5 + - - +
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Residues in contact with LYS 203 (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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28D ARG* 4.7 1.6 - - - +
30D ILE* 4.0 8.0 - - + +
121D GLU* 2.7 38.8 + - - -
129D PHE* 3.4 44.4 - - + -
202D ASN* 1.3 72.1 - - - +
204D LEU* 1.3 66.8 + - - +
207D LYS* 3.0 20.8 + - - +
289D ASP* 3.6 10.7 + - - +
291D SER* 3.1 31.7 + - - +
292D PRO 3.3 11.1 + - - +
293D VAL* 3.7 28.7 - - + -
294D ILE* 4.6 2.4 - - - +
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Residues in contact with LEU 204 (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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202D ASN* 3.1 5.1 - - - +
203D LYS* 1.3 74.7 - - - +
205D LEU* 1.3 60.4 + - + +
207D LYS* 3.7 3.6 - - - +
208D LEU* 3.0 40.1 + - + +
230D ILE* 4.9 0.2 - - + -
239D ILE* 4.2 9.0 - - + -
240D PRO* 3.6 38.4 - - + +
284D LEU* 3.4 46.2 - - + +
287D GLY* 3.9 21.3 - - - -
288D GLU 4.3 1.6 - - - +
289D ASP* 2.8 24.4 + - + +
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Residues in contact with LEU 205 (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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200D ALA* 3.6 10.3 - - + -
201D SER* 3.9 16.2 - - - +
202D ASN* 2.8 26.2 - - - +
204D LEU* 1.3 73.9 - - + +
206D ALA* 1.3 58.3 + - - +
208D LEU* 3.8 4.2 - - + +
209D VAL* 2.9 33.6 + - - +
221D LEU* 3.6 27.8 - - + -
226D CYS* 3.8 28.7 - - + -
229D LEU* 4.2 7.8 - - + +
230D ILE* 4.2 13.9 - - + -
287D GLY* 3.4 29.4 - - - +
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Residues in contact with ALA 206 (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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30D ILE* 3.7 23.6 - - + +
32D HIS* 3.5 13.9 - - + +
129D PHE* 4.8 0.4 - - + -
198D GLY* 3.7 17.0 - - - +
200D ALA* 3.5 9.9 - - - +
202D ASN 3.0 18.3 + - - +
203D LYS 3.9 3.8 - - - +
205D LEU* 1.3 76.0 - - - +
207D LYS* 1.3 58.6 + - - +
209D VAL* 3.5 5.6 - - - +
210D SER* 3.0 31.7 + - - -
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Residues in contact with LYS 207 (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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32D HIS* 3.7 18.3 - - + +
34D ASP* 5.2 0.6 + - - -
123D LEU* 3.8 23.6 - - + -
127D GLU* 2.8 27.8 + - - +
129D PHE* 3.9 14.8 - - + -
203D LYS 3.0 18.6 + - - +
204D LEU* 3.7 4.0 - - - +
206D ALA* 1.3 74.5 - - - +
208D LEU* 1.3 64.1 + - - +
210D SER* 3.2 14.2 + - - -
211D GLY* 4.0 2.9 + - - -
240D PRO* 4.0 31.4 - - + -
872E A 3.9 3.8 - - - -
873E G 2.7 29.4 + - - -
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Residues in contact with LEU 208 (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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204D LEU* 3.0 40.2 + - + +
205D LEU* 3.9 2.9 - - + +
207D LYS* 1.3 76.5 - - - +
209D VAL* 1.3 62.6 + - - +
210D SER 3.6 0.2 + - - -
211D GLY* 3.7 8.5 + - - -
212D VAL* 4.0 8.8 - - - +
229D LEU* 3.9 25.3 - - + +
230D ILE* 3.7 27.4 - - + -
233D LEU* 4.1 27.4 - - + -
238D GLU 3.8 11.0 - - - +
239D ILE* 5.9 0.7 - - + -
240D PRO* 3.8 23.1 - - + -
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Residues in contact with VAL 209 (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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158D TYR* 3.9 20.0 - - + -
198D GLY* 3.5 15.9 - - - -
199D VAL 3.8 15.5 - - - +
205D LEU 2.9 20.7 + - - +
206D ALA* 3.5 8.1 - - - +
208D LEU* 1.3 73.8 - - - +
210D SER* 1.3 69.5 + - - +
211D GLY 3.1 2.7 - - - -
212D VAL* 3.1 26.3 + - + +
219D THR* 3.5 33.6 - - + +
221D LEU* 3.9 13.2 - - + +
229D LEU* 4.1 9.9 - - + -
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Residues in contact with SER 210 (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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32D HIS* 2.8 32.0 + - - -
34D ASP* 4.4 4.8 + - - +
196D CYS* 3.6 23.6 - - - +
197D ALA* 3.5 10.1 - - - +
198D GLY* 3.1 32.3 - - - +
206D ALA 3.0 11.7 + - - -
207D LYS 3.2 6.8 + - - -
209D VAL* 1.3 76.2 - - - +
211D GLY* 1.3 61.5 + - - +
212D VAL 3.5 0.7 + - - -
213D PHE 3.9 7.4 + - - +
217D GLN 5.0 0.2 - - - +
219D THR* 4.9 1.2 + - - -
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Residues in contact with GLY 211 (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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34D ASP* 6.1 0.9 - - - -
196D CYS* 5.7 0.7 - - - -
207D LYS 4.0 2.5 + - - -
208D LEU 3.7 7.6 + - - -
209D VAL 3.1 1.4 - - - -
210D SER* 1.3 83.3 + - - +
212D VAL* 1.3 62.9 + - - +
213D PHE 3.5 0.9 - - - -
214D LYS* 3.3 30.5 - - - +
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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