Contacts of the helix formed by residues 195 - 206 (chain G) in PDB entry 4GEK
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 ILE 195 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G TRP* 3.9 26.7 - - + -
23G ARG* 3.4 39.0 - - + +
24G VAL* 4.1 20.2 - - + -
27G VAL* 4.1 19.0 - - + +
31G MET* 3.7 31.9 - - + -
193G LEU* 3.1 13.6 - - + -
194G GLU* 1.3 78.3 - - - +
196G SER* 1.3 62.4 + - - +
197G GLN 3.4 1.1 - - - -
198G LYS* 3.2 12.9 + - + +
199G ARG* 2.8 26.7 + - + +
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Residues in contact with SER 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G TYR* 2.8 63.7 + - - -
191G SER* 3.7 14.2 + - - -
193G LEU* 2.8 21.9 + - - -
194G GLU 3.1 0.6 + - - -
195G ILE* 1.3 83.1 - - - +
197G GLN* 1.3 59.9 + - - +
199G ARG 3.3 0.2 + - - -
200G SER* 2.9 17.8 + - - -
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Residues in contact with GLN 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G GLU 4.3 4.2 + - - +
195G ILE 3.4 0.6 - - - -
196G SER* 1.3 80.4 + - - +
198G LYS* 1.3 59.8 + - + +
200G SER* 3.2 11.1 + - - -
201G MET* 2.9 61.4 + - - +
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Residues in contact with LYS 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ASP* 6.1 2.7 - - - +
18G TRP* 3.7 23.8 - - + +
23G ARG* 3.0 33.7 - - - +
194G GLU 5.2 2.2 + - - +
195G ILE* 3.2 14.1 + - + +
197G GLN* 1.3 78.6 - - + +
199G ARG* 1.3 57.0 + - - +
201G MET* 3.2 19.7 + - + +
202G LEU 2.9 23.7 + - - -
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Residues in contact with ARG 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G TRP* 3.6 10.8 - - + -
31G MET* 3.6 46.6 - - + +
32G ILE* 3.9 3.7 - - - +
35G SER* 4.0 4.6 + - - +
36G VAL* 3.9 24.9 - - - +
136G GLN* 5.5 2.6 - - - +
137G PHE* 4.8 0.2 - - - -
190G TYR* 3.2 21.8 - - + +
195G ILE 2.8 19.8 + - - +
196G SER* 4.3 2.2 - - - -
198G LYS* 1.3 73.3 - - - +
200G SER* 1.3 62.9 + - - +
202G LEU* 3.3 24.1 + - - +
203G GLU* 3.0 50.9 + - - +
206G MET* 6.1 1.1 - - - -
235G PHE* 5.5 2.8 - - - -
303G GEK 3.0 37.9 + - - -
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Residues in contact with SER 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G LYS* 4.6 8.8 + - - +
190G TYR* 3.0 26.2 + - - -
196G SER 2.9 15.1 + - - -
197G GLN* 3.5 12.3 - - - -
199G ARG* 1.3 72.3 - - - +
201G MET* 1.3 60.2 - - - +
203G GLU* 3.2 9.3 + - - +
204G ASN* 2.9 42.8 + - - +
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Residues in contact with MET 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ASP* 5.6 11.4 - - + +
197G GLN* 2.9 46.1 + - - +
198G LYS* 3.2 22.4 + - + +
200G SER* 1.3 74.2 - - - +
202G LEU* 1.3 63.7 + - - +
204G ASN* 2.9 21.9 + - - +
205G VAL* 3.3 16.5 + - - +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU 4.1 22.4 - - - +
18G TRP* 3.8 48.2 - - + -
20G PHE* 5.0 0.4 - - + -
137G PHE* 4.0 24.0 - - + -
198G LYS 2.9 13.1 + - - +
199G ARG* 3.4 31.0 - - - +
201G MET* 1.3 75.7 - - - +
203G GLU* 1.3 62.8 + - - +
205G VAL* 3.0 20.0 + - + +
206G MET* 3.0 32.5 + - + +
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Residues in contact with GLU 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G SER* 4.3 12.1 + - - +
165G LYS* 2.8 45.3 + - + +
181G HIS* 3.5 19.8 - - - -
185G LYS* 5.2 3.5 + - - +
190G TYR* 4.8 1.9 + - - -
199G ARG* 3.0 55.1 + - - +
200G SER* 3.2 10.5 + - - +
202G LEU* 1.3 74.6 - - + +
204G ASN* 1.3 66.1 + - - +
205G VAL 3.2 1.2 + - - -
206G MET* 3.4 29.7 + - + +
235G PHE* 4.2 2.8 - - - -
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Residues in contact with ASN 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G LYS* 6.0 0.2 + - - -
178G PHE* 5.5 6.8 - - - -
200G SER* 2.9 26.8 + - - +
201G MET* 2.9 15.2 + - - +
203G GLU* 1.3 81.2 - - - +
205G VAL* 1.3 61.7 + - + +
206G MET 4.9 1.2 - - - +
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Residues in contact with VAL 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.0 39.6 - - + +
16G GLY* 4.4 6.5 - - - +
201G MET 3.3 11.2 + - - +
202G LEU* 3.0 18.0 + - + +
204G ASN* 1.3 82.6 - - + +
206G MET* 1.3 66.8 + - - +
207G LEU* 3.6 14.1 + - - +
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Residues in contact with MET 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU 5.4 3.6 - - - +
136G GLN* 3.5 55.2 - - + +
137G PHE* 4.0 19.1 - - + -
165G LYS* 5.6 5.6 - - + -
199G ARG* 6.0 1.3 - - - -
202G LEU* 3.0 45.7 + - + +
203G GLU* 3.4 23.0 + - + +
204G ASN 4.9 1.2 - - - -
205G VAL* 1.3 81.5 - - + +
207G LEU* 1.3 63.3 + - - +
208G THR* 3.7 16.5 + - + +
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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