Contacts of the strand formed by residues 164 - 178 (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 ARG 164 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149G LYS 3.4 8.5 - - - +
150G GLN* 3.4 48.3 - - + +
151G PHE 4.2 9.4 + - - +
159G ASN* 3.9 25.7 + - - +
162G ALA* 2.9 27.5 + - - +
163G TYR* 1.3 75.7 - - - +
165G ALA* 1.3 60.8 + - - +
166G GLN* 3.8 21.1 - - - +
191G LYS 3.5 0.3 - - - +
192G PHE* 3.2 28.6 - - - -
193G THR* 3.0 19.9 + - - +
194G SER* 3.9 3.0 - - - +
195G VAL* 3.3 45.1 - - - +
114H LEU* 4.1 5.4 - - - -
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Residues in contact with ALA 165 (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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147G SER 4.0 0.2 - - - +
148G SER* 3.5 8.7 + - - -
149G LYS* 2.9 46.2 + - + +
164G ARG* 1.3 70.5 - - - +
166G GLN* 1.3 60.9 + - - +
167G PRO* 3.8 4.7 - - - +
168G GLN* 3.7 36.1 - - + +
190G ALA* 5.5 0.2 - - + -
191G LYS 3.8 3.6 - - - -
192G PHE* 4.1 9.2 - - + -
114H LEU* 4.0 9.5 - - + +
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Residues in contact with GLN 166 (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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148G SER* 5.1 9.4 - - - +
150G GLN* 4.9 7.7 + - - +
164G ARG* 4.1 19.8 - - + +
165G ALA* 1.3 76.1 - - - +
167G PRO* 1.3 63.1 - - + +
191G LYS* 2.8 39.4 + - - +
193G THR* 4.0 20.0 + - + +
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Residues in contact with PRO 167 (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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146G LEU* 4.1 23.6 - - + -
147G SER 3.5 13.5 - - - +
148G SER* 5.1 2.9 - - - -
166G GLN* 1.3 89.7 + - + +
168G GLN* 1.3 61.0 + - - +
169G LEU* 6.3 0.4 - - + -
189G ALA 3.8 2.2 - - - +
190G ALA* 3.3 3.3 - - - +
191G LYS* 3.0 36.6 + - + -
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Residues in contact with GLN 168 (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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145G THR 3.5 2.8 - - - +
146G LEU* 3.6 3.9 - - - +
147G SER* 2.9 44.7 + - - +
149G LYS* 3.2 30.5 + - - +
165G ALA* 3.7 27.0 + - + +
167G PRO* 1.3 77.3 - - - +
169G LEU* 1.3 61.2 + - - +
170G ASP* 3.1 22.8 - - - +
188G GLN* 3.6 23.2 + - + +
189G ALA 3.6 1.8 - - - -
190G ALA* 3.9 14.1 - - + +
192G PHE* 4.5 11.9 - - - -
304G ASP* 4.9 5.9 + - - +
114H LEU* 5.1 2.4 - - - +
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Residues in contact with LEU 169 (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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144G ALA* 4.7 4.3 - - + -
145G THR 3.3 27.6 - - - +
146G LEU* 4.2 19.3 - - + +
167G PRO* 6.3 0.7 - - + -
168G GLN* 1.3 73.3 - - - +
170G ASP* 1.3 63.9 + - - +
171G MET* 4.2 25.5 + - + -
188G GLN* 3.1 9.8 - - - +
189G ALA* 2.9 52.1 + - + +
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Residues in contact with ASP 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ASN* 4.0 1.4 - - - +
144G ALA* 3.2 3.5 - - - -
145G THR* 2.8 50.7 + - - +
147G SER* 5.4 3.3 + - - -
149G LYS* 5.0 1.6 + - - -
168G GLN* 3.1 19.7 - - - +
169G LEU* 1.3 73.4 - - - +
171G MET* 1.3 62.3 + - - +
172G ASN* 4.8 5.2 - - - +
186G TYR* 2.8 19.8 + - + -
187G GLY 3.6 1.8 - - - -
188G GLN* 2.7 33.7 + - - +
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Residues in contact with MET 171 (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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142G TRP* 3.7 31.4 - - + -
143G ASN 3.3 4.0 - - - +
144G ALA* 3.7 13.5 - - + -
169G LEU* 4.2 23.8 - - + -
170G ASP* 1.3 79.0 - - - +
172G ASN* 1.3 65.1 + - - +
185G VAL 4.0 0.6 - - - +
186G TYR* 3.3 8.5 - - - -
187G GLY* 2.9 40.7 + - - +
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Residues in contact with ASN 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142G TRP* 3.1 8.1 - - - +
143G ASN* 2.9 55.0 + - - +
170G ASP* 4.8 4.4 - - - +
171G MET* 1.3 81.6 + - - +
173G TYR* 1.3 61.3 + - - +
174G TYR* 3.6 28.3 + - + -
184G HIS* 3.1 21.9 + - + -
185G VAL 3.5 3.4 - - - -
186G TYR* 3.2 26.1 - - - -
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Residues in contact with TYR 173 (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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141G ASN* 3.7 17.7 - - + -
142G TRP* 4.1 12.3 - + + -
172G ASN* 1.3 74.5 - - - +
174G TYR* 1.3 77.8 + - - +
175G LYS* 3.4 34.2 + - + +
183G MET* 5.8 2.7 - - + -
184G HIS* 3.3 6.7 + - - -
185G VAL* 2.9 54.9 + - + +
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Residues in contact with TYR 174 (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 GLU 4.9 2.2 - - - +
141G ASN* 2.7 35.3 + - - +
143G ASN* 3.8 8.7 + - - -
172G ASN* 3.6 28.6 + - + +
173G TYR* 1.3 87.8 - - - +
175G LYS* 1.3 63.7 + - - +
176G ASN* 5.5 5.4 - - - +
183G MET 3.7 3.6 - - - +
184G HIS* 3.1 43.6 - + + -
30H ARG* 3.2 56.9 - - - +
34H GLN* 4.4 15.7 - - - -
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Residues in contact with LYS 175 (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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141G ASN* 5.8 3.1 - - - +
173G TYR* 3.4 29.7 + - + +
174G TYR* 1.3 77.4 - - - +
176G ASN* 1.3 70.3 + - - +
178G VAL* 3.6 31.5 - - + +
183G MET* 2.9 43.5 + - + +
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Residues in contact with ASN 176 (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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174G TYR* 5.5 4.0 - - - +
175G LYS* 1.3 82.1 + - - +
177G ASP* 1.3 78.7 + - - +
178G VAL* 3.2 6.9 + - - +
182G ASP* 3.4 23.6 - - - +
183G MET 5.3 0.5 - - - +
34H GLN* 6.0 4.9 + - - +
37H ARG* 4.0 25.8 - - - +
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Residues in contact with ASP 177 (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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176G ASN* 1.3 80.0 - - - +
178G VAL* 1.3 60.4 + - - +
179G GLY* 2.9 18.6 + - - +
180G PRO 5.7 0.2 - - - -
181G PHE 3.6 4.0 - - - -
182G ASP* 3.1 10.7 + - - -
602G C8E 5.9 2.8 - - - +
37H ARG* 2.7 30.3 + - - -
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Residues in contact with VAL 178 (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* 3.6 56.8 - - + +
176G ASN 4.0 0.2 - - - +
177G ASP* 1.3 71.5 - - - +
179G GLY* 1.3 62.2 + - - +
180G PRO 3.5 0.5 - - - -
181G PHE* 2.9 29.5 + - - +
183G MET* 3.7 39.0 - - + -
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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