Contacts of the helix formed by residues 180 - 192 (chain G) in PDB entry 3IYD
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 ARG 180 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G LYS* 5.8 4.8 - - - +
169G ARG* 3.8 34.5 + - - +
170G GLN* 4.0 31.5 - - + +
179G SER* 1.3 73.6 - - - +
181G GLU* 1.3 93.3 + - + +
182G THR 3.4 0.2 - - - -
183G VAL* 3.7 5.2 + - - +
184G GLY* 3.5 13.9 + - - -
74J T 3.4 44.6 + - - +
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Residues in contact with GLU 181 (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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179G SER* 3.3 20.8 - - - +
180G ARG* 1.3 116.5 + - + +
182G THR* 1.3 65.9 + - - +
184G GLY* 3.2 2.8 + - - -
185G ARG* 3.0 53.6 + - - +
21I T 4.0 25.3 + - + -
22I C 5.0 7.9 + - - +
75J G 5.7 8.1 - - + +
76J T 6.5 0.2 - - + -
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Residues in contact with THR 182 (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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139G VAL* 3.8 28.7 - - + -
178G CYS* 4.9 2.5 - - - -
179G SER* 2.9 22.8 + - - -
181G GLU* 1.3 78.5 - - - +
183G VAL* 1.3 62.7 + - - +
185G ARG* 4.6 6.4 + - - +
186G ILE* 3.1 47.5 + - + +
19I G 3.7 20.9 - - + +
20I A 3.0 24.3 + - - +
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Residues in contact with VAL 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ILE* 3.8 29.4 - - + +
169G ARG* 3.6 31.9 - - + +
172G ILE* 3.8 26.7 - - + -
173G GLY 4.5 0.9 - - - +
178G CYS* 3.6 18.8 - - - -
179G SER 3.2 18.8 - - - +
180G ARG 3.7 7.2 + - - +
181G GLU 3.2 0.4 - - - -
182G THR* 1.3 77.4 - - - +
184G GLY* 1.3 56.5 + - - +
186G ILE* 4.1 2.4 - - - +
187G LEU* 3.0 30.8 + - + +
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Residues in contact with GLY 184 (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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169G ARG* 3.6 21.3 - - - +
180G ARG 3.5 5.1 + - - -
181G GLU 3.2 6.0 + - - -
183G VAL* 1.3 78.9 - - - +
185G ARG* 1.3 64.3 + - - +
186G ILE 3.2 0.2 - - - -
187G LEU* 3.1 14.6 + - - +
188G LYS* 3.2 20.3 + - - +
75J G 4.9 14.6 - - - -
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Residues in contact with ARG 185 (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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181G GLU* 3.0 41.0 + - - +
182G THR* 4.1 5.6 - - - +
184G GLY* 1.3 74.6 - - - +
186G ILE* 1.3 68.5 + - + +
188G LYS* 3.8 5.4 + - - +
189G MET* 3.4 23.8 + - + +
20I A 3.0 37.8 + - - +
21I T 3.0 33.9 + - - +
22I C 4.6 4.9 - - - +
75J G 5.5 13.2 - - + +
76J T 4.2 20.3 + - - +
77J G 3.1 21.1 + - - -
78J A 4.9 0.6 - - - +
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Residues in contact with ILE 186 (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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139G VAL* 5.1 7.6 - - + -
140G THR* 4.1 32.5 - - + +
143G ILE* 5.6 5.6 - - + -
182G THR* 3.1 36.9 + - + +
183G VAL* 4.3 2.7 - - - +
185G ARG* 1.3 85.2 - - + +
187G LEU* 1.3 68.0 + - - +
188G LYS 3.2 0.2 - - - -
189G MET* 2.9 40.5 + - + +
190G LEU* 3.3 19.2 + - + +
18I A 6.3 1.8 - - + -
19I G 5.3 9.6 - - + +
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Residues in contact with LEU 187 (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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143G ILE* 6.4 1.8 - - + -
147G LEU* 5.8 3.6 - - + -
169G ARG* 3.6 33.0 - - + +
183G VAL* 3.0 22.0 + - + +
184G GLY* 3.1 8.0 + - - +
186G ILE* 1.3 80.8 - - - +
188G LYS* 1.3 62.9 + - + +
190G LEU* 3.7 5.9 + - - -
191G GLU* 3.5 13.1 - - - +
196G ILE* 3.6 29.4 - - + +
198G ALA* 3.8 26.0 - - + -
203G ILE* 4.0 33.4 - - + -
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Residues in contact with LYS 188 (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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169G ARG* 6.2 0.4 - - - +
184G GLY 3.2 14.7 + - - +
185G ARG* 4.2 4.0 - - - +
187G LEU* 1.3 78.6 - - + +
189G MET* 1.3 64.1 + - - +
190G LEU 3.2 1.1 - - - -
191G GLU* 3.2 42.5 + - - +
192G ASP* 3.7 12.5 - - - +
198G ALA* 5.7 3.4 - - + -
75J G 3.0 58.8 + - - -
76J T 4.5 11.6 + - - +
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Residues in contact with MET 189 (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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140G THR* 6.1 0.2 - - - -
185G ARG* 3.4 18.3 + - + +
186G ILE* 2.9 38.3 + - + +
188G LYS* 1.3 79.5 - - - +
190G LEU* 1.3 63.8 + - + +
191G GLU 3.5 0.5 + - - -
192G ASP* 3.6 19.2 + - - +
193G GLN* 4.0 19.6 - - - +
18I A 5.0 13.0 - - - +
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Residues in contact with LEU 190 (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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140G THR* 5.0 18.6 - - + -
144G ALA* 6.4 1.6 - - + -
147G LEU* 5.9 4.0 - - + -
186G ILE* 3.3 21.9 + - + +
187G LEU* 3.7 1.3 + - - +
188G LYS 3.2 0.2 - - - -
189G MET* 1.3 81.4 - - + +
191G GLU* 1.3 64.8 + - - +
192G ASP 3.3 0.4 - - - -
193G GLN* 3.3 18.6 + - - +
194G ASN 3.3 0.2 + - - -
195G LEU* 3.2 48.4 + - + +
196G ILE* 3.8 36.8 - - + -
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Residues in contact with GLU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G LEU 3.5 12.9 - - - +
188G LYS* 3.3 36.2 - - - +
189G MET 3.2 0.8 - - - -
190G LEU* 1.3 76.9 - - - +
192G ASP* 1.3 66.0 + - - +
194G ASN* 3.1 13.5 + - - +
196G ILE* 4.0 23.8 - - + +
197G SER* 4.5 3.4 - - - -
198G ALA* 3.3 40.6 + - - +
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Residues in contact with ASP 192 (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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188G LYS 3.7 14.1 - - - +
189G MET* 3.6 11.5 + - - +
190G LEU 3.3 0.6 - - - -
191G GLU* 1.3 80.7 - - - +
193G GLN* 1.3 61.4 + - + +
194G ASN* 3.2 2.5 + - - +
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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