Contacts of the helix formed by residues 198 - 209 (chain D) in PDB entry 3G4C
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 CYS 198 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D VAL* 5.5 0.2 - - - -
18D GLY 5.3 0.7 - - - -
19D ASN* 4.2 13.9 - - - -
20D ASP* 3.2 22.0 - - - +
60D ILE* 3.7 33.4 - - - -
62D PHE* 3.9 15.3 - - - -
194D PHE* 2.9 23.0 + - + +
195D LYS 3.6 2.5 - - - -
197D LYS* 1.3 83.7 - - - +
199D PRO* 1.3 60.6 - - - +
201D THR* 4.1 3.4 - - - -
202D PHE* 3.0 27.0 + - - +
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Residues in contact with PRO 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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20D ASP* 3.3 8.5 - - - +
42D ARG* 4.5 1.5 + - - +
195D LYS* 3.2 22.4 - - + +
196D GLU 4.0 6.5 - - - +
197D LYS 3.6 6.3 - - - +
198D CYS* 1.3 87.8 - - - +
200D TRP* 1.3 72.7 + - + +
202D PHE* 3.9 3.5 - - + +
203D GLU* 2.9 31.7 + - - +
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Residues in contact with TRP 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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20D ASP* 3.1 21.1 + - + +
21D LEU* 3.8 27.6 - - + -
39D GLU* 5.0 12.1 - - + -
41D ASP* 4.2 14.4 - - + -
42D ARG* 3.3 58.4 + - + +
45D ILE* 3.6 30.1 - - + +
46D GLU* 5.2 1.9 - - - +
199D PRO* 1.3 84.1 - - + +
201D THR* 1.3 61.1 + - - +
203D GLU* 3.4 1.7 + - - +
204D ALA* 3.0 30.7 + - - +
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Residues in contact with THR 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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20D ASP* 2.7 31.1 + - - +
45D ILE* 3.8 12.7 - - - +
49D MET* 3.8 19.5 - - + +
57D PHE* 3.8 26.3 - - + -
60D ILE* 4.3 4.6 - - + +
164D ALA* 5.3 0.4 - - + -
168D MET* 4.2 4.7 - - + -
194D PHE* 3.7 21.3 - - + -
198D CYS* 3.9 8.7 - - - +
200D TRP* 1.3 74.6 - - - +
202D PHE* 1.3 60.7 + - - +
204D ALA 3.9 0.2 - - - -
205D PHE* 2.9 27.4 + - - +
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Residues in contact with PHE 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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171D LEU* 4.8 2.5 - - + -
191D ALA* 3.7 34.3 - - + -
194D PHE* 3.7 26.2 - + + -
195D LYS* 3.5 52.0 - - + +
198D CYS 3.0 20.0 + - - +
199D PRO 3.9 3.4 - - - +
201D THR* 1.3 77.0 - - - +
203D GLU* 1.3 67.4 + - + +
205D PHE* 3.4 9.1 - + - +
206D LEU* 3.0 55.9 + - + +
215D LEU* 4.5 13.2 - - + -
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Residues in contact with GLU 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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42D ARG* 3.0 28.3 - - - +
46D GLU* 4.8 0.7 - - - +
199D PRO 2.9 19.9 + - - +
200D TRP 3.8 3.4 - - - +
202D PHE* 1.3 83.3 - - + +
204D ALA* 1.3 56.6 + - - +
206D LEU* 3.4 6.5 + - - +
207D LYS* 3.1 65.2 + - + +
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Residues in contact with ALA 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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45D ILE* 3.9 19.5 - - + -
46D GLU* 4.0 31.3 + - + -
49D MET* 3.6 9.4 - - + -
200D TRP 3.0 17.4 + - - +
201D THR* 4.0 1.8 - - - +
203D GLU* 1.3 71.4 - - - +
205D PHE* 1.3 60.8 + - - +
207D LYS* 4.3 2.7 - - - -
208D TYR* 2.8 42.5 + - + +
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Residues in contact with PHE 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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49D MET* 3.7 9.9 - - - +
168D MET* 3.5 55.4 - - + -
171D LEU* 4.2 21.3 - - + -
172D ASN* 3.4 30.5 - - - -
194D PHE* 4.7 1.8 - + - -
201D THR 2.9 20.1 + - - +
202D PHE* 3.4 16.4 - + - +
204D ALA* 1.3 74.3 - - - +
206D LEU* 1.3 71.0 + - + +
209D ALA* 2.9 17.4 + - + -
210D TYR* 2.8 55.7 + + + -
215D LEU* 4.7 0.9 - - + -
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Residues in contact with LEU 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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202D PHE* 3.0 41.9 + - + +
203D GLU* 3.7 9.9 - - + +
205D PHE* 1.3 85.6 - - + +
207D LYS* 1.3 62.9 + - + +
208D TYR 5.1 0.2 - - - -
210D TYR* 3.6 43.2 + - + +
215D LEU* 4.0 35.9 - - + +
216D LYS* 5.2 14.1 - - + +
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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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42D ARG* 5.2 1.0 - - - +
46D GLU* 3.1 29.9 + - - +
203D GLU* 3.1 47.6 + - + +
204D ALA 3.2 3.8 + - - +
206D LEU* 1.3 79.5 - - + +
208D TYR* 1.3 86.3 + - + +
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Residues in contact with TYR 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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46D GLU* 3.7 52.4 + - + +
49D MET* 3.9 11.7 - - + +
50D LYS* 3.9 46.0 - - + +
204D ALA* 2.8 31.6 + - + +
207D LYS* 1.3 98.8 - - + +
209D ALA* 1.3 57.7 - - - +
210D TYR 3.8 1.1 - - - -
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Residues in contact with ALA 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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49D MET* 3.7 37.7 - - + +
54D GLU* 6.5 1.1 - - + -
172D ASN* 3.9 6.6 + - - +
205D PHE* 2.9 15.9 + - + +
208D TYR* 1.3 74.3 - - - +
210D TYR* 1.3 66.6 + - - +
211D LYS* 3.3 15.8 + - - +
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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