Contacts of the strand formed by residues 181 - 193 (chain G) in PDB entry 5IXM
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 181 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386E THR* 5.2 4.9 - - + -
603E C8E 3.5 53.4 - - - -
177G ASP* 3.4 2.1 + - - -
178G VAL* 2.9 35.9 + - - +
179G GLY 3.2 1.0 - - - -
180G PRO* 1.3 108.6 - - + +
182G ASP* 1.3 68.5 - - - +
183G MET* 4.2 12.6 - - + -
211G VAL* 3.7 29.4 - - + -
212G ASN 3.2 11.9 - - - +
213G LEU* 4.1 12.8 - - + -
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Residues in contact with ASP 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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175G LYS 3.7 2.9 - - - -
176G ASN* 3.4 16.1 - - - +
177G ASP 3.1 14.6 + - - -
180G PRO 4.3 0.4 + - - +
181G PHE* 1.3 74.0 - - - +
183G MET* 1.3 64.0 + - - +
210G THR 3.9 0.7 - - - +
211G VAL* 3.7 1.0 - - - -
212G ASN* 2.9 46.7 + - + +
214G PRO* 3.7 13.3 - - - +
37H ARG* 2.3 48.1 + - - -
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Residues in contact with MET 183 (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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173G TYR* 4.7 2.9 - - + -
174G TYR* 3.7 1.4 - - - +
175G LYS* 2.9 41.0 + - + +
176G ASN* 5.3 0.7 - - - +
178G VAL* 3.7 43.3 - - + +
181G PHE* 4.7 8.3 - - + -
182G ASP* 1.3 79.9 - - - +
184G HIS* 1.3 64.5 + - - +
185G VAL* 5.8 3.1 - - + -
210G THR 3.4 4.3 - - - +
211G VAL* 4.3 32.1 - - + -
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Residues in contact with HIS 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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172G ASN* 3.1 28.7 + - + -
173G TYR* 3.3 11.6 + - - -
174G TYR* 3.1 40.6 + + + -
183G MET* 1.3 77.6 - - - +
185G VAL* 1.3 73.6 + - - +
186G TYR* 4.0 11.7 - - + +
208G GLU* 3.7 3.8 - - - +
209G PRO 3.7 0.3 - - - -
210G THR* 2.9 52.2 + - + +
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Residues in contact with VAL 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G MET 4.0 0.5 - - - +
172G ASN* 3.5 3.1 - - - -
173G TYR* 2.9 53.5 + - + +
183G MET* 6.0 2.7 - - + -
184G HIS* 1.3 81.6 - - - +
186G TYR* 1.3 63.9 + - - +
207G ILE* 3.8 29.4 - - + -
208G GLU 3.5 10.3 - - - +
209G PRO* 4.1 17.3 - - + -
210G THR 4.9 0.4 - - - +
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Residues in contact with TYR 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G ASP* 2.8 17.7 + - + -
171G MET 3.3 10.3 - - - -
172G ASN* 3.2 31.6 - - - +
184G HIS* 4.0 11.2 + - + +
185G VAL* 1.3 77.3 - - - +
187G GLY* 1.3 69.6 + - - +
188G GLN* 2.7 37.3 + - + -
206G HIS* 4.1 17.9 - + - -
207G ILE* 3.6 3.1 - - - +
208G GLU* 2.9 63.4 + - + +
324G LEU* 4.8 6.2 - - + +
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Residues in contact with GLY 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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170G ASP* 3.6 0.3 - - - -
171G MET* 2.9 40.6 + - - +
186G TYR* 1.3 83.3 - - - +
188G GLN* 1.3 63.2 + - - +
206G HIS 3.2 9.9 - - - -
207G ILE* 4.2 9.4 - - - -
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Residues in contact with GLN 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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168G GLN* 3.6 22.5 + - + -
169G LEU 3.1 8.1 - - - +
170G ASP* 2.7 24.7 + - - +
186G TYR* 2.7 24.4 + - + +
187G GLY* 1.3 74.6 - - - +
189G ALA* 1.3 71.3 + - - +
190G ALA* 4.2 4.1 - - - +
204G ARG* 2.6 39.2 + - - +
205G PHE* 3.5 4.3 - - - -
206G HIS* 2.9 41.0 + - + +
304G ASP* 5.5 1.0 + - - -
324G LEU* 3.9 7.6 - - - +
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Residues in contact with ALA 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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167G PRO* 3.8 2.6 - - - +
168G GLN* 3.6 1.4 - - - -
169G LEU* 2.9 51.2 + - + +
188G GLN* 1.3 74.6 - - - +
190G ALA* 1.3 59.6 + - - +
204G ARG 3.3 4.9 - - - +
205G PHE* 4.1 23.8 - - + -
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Residues in contact with ALA 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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165G ALA* 5.5 0.2 - - + -
167G PRO 3.3 5.6 - - - +
168G GLN* 3.9 19.5 - - + -
188G GLN* 4.2 9.2 - - - +
189G ALA* 1.3 75.7 - - - +
191G LYS* 1.3 60.1 + - - +
192G PHE* 3.7 32.5 - - + -
202G ALA 3.8 0.7 - - - +
203G SER* 3.5 3.5 - - - -
204G ARG* 2.9 36.5 + - - +
205G PHE* 6.0 0.2 - - - -
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Residues in contact with LYS 191 (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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164G ARG 3.5 1.2 - - - +
165G ALA 3.8 0.2 - - - -
166G GLN* 2.8 52.1 + - - +
167G PRO* 3.0 18.2 + - + +
190G ALA* 1.3 72.3 - - - +
192G PHE* 1.3 64.1 + - - +
193G THR* 3.8 20.8 + - + +
201G GLU* 5.9 0.9 - - + +
202G ALA 3.4 7.9 - - - +
203G SER* 3.6 20.2 - - - +
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Residues in contact with PHE 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G TYR* 4.2 6.9 - - + -
164G ARG 3.2 16.2 - - - +
165G ALA* 4.1 14.8 - - + -
168G GLN* 4.5 4.7 - - - -
190G ALA* 3.7 20.2 - - + -
191G LYS* 1.3 72.3 - - - +
193G THR* 1.3 63.8 + - - +
201G GLU* 3.5 3.6 - - - -
202G ALA* 2.9 43.4 + - + +
204G ARG* 3.4 53.8 - - + -
303G TYR* 3.5 39.3 - + + -
304G ASP* 3.9 12.6 - - + -
114H LEU* 3.6 25.4 - - + -
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Residues in contact with THR 193 (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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163G TYR* 3.7 4.2 - - - -
164G ARG* 3.0 35.0 + - - +
166G GLN* 4.0 23.7 + - + +
191G LYS* 3.8 24.4 + - + +
192G PHE* 1.3 80.1 - - - +
194G SER* 1.3 64.6 + - - +
201G GLU* 3.6 36.3 - - + +
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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