Contacts of the helix formed by residues 172 - 185 (chain O) in PDB entry 3EXG
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 GLN 172 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177M GLU* 3.6 5.1 + - - -
57N ILE* 3.1 26.3 + - - +
58N SER* 3.9 1.2 - - - +
59N GLU* 3.1 25.7 + - - +
88N GLN* 3.0 14.3 + - - +
138O VAL* 2.8 29.7 + - + +
139O GLY* 4.2 4.5 - - - -
169O ALA 3.1 17.0 + - - +
171O ASN* 1.3 79.3 - - - +
173O GLY* 1.3 65.4 + - - +
174O GLN* 2.7 36.9 + - + +
175O ILE* 3.0 28.0 + - + +
176O PHE* 3.8 6.6 + - - -
60P MET* 5.4 0.3 - - - +
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Residues in contact with GLY 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLY* 3.5 36.2 - - - -
177M GLU* 2.5 25.0 + - - -
171O ASN 3.2 1.8 + - - -
172O GLN* 1.3 69.6 - - - +
174O GLN* 1.3 64.1 + - - +
176O PHE* 2.8 20.9 + - - -
177O GLU 3.2 7.4 + - - -
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Residues in contact with GLN 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLY* 4.5 0.2 - - - -
88N GLN* 2.8 18.2 + - - -
138O VAL 3.4 0.2 + - - -
139O GLY 3.3 28.8 - - - +
140O ALA* 3.3 14.6 - - - +
143O PRO* 3.4 26.3 - - + +
172O GLN* 2.7 31.1 + - + +
173O GLY* 1.3 71.5 - - - +
175O ILE* 1.3 62.8 + - - +
177O GLU* 3.4 16.1 + - - +
178O ALA* 3.0 22.2 + - - +
60P MET* 3.4 35.8 - - + +
92P GLN* 3.5 3.6 + - - -
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Residues in contact with ILE 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139O GLY* 4.5 6.5 - - - +
142O VAL* 3.4 36.6 - - + -
165O TYR* 3.8 26.7 - - + -
169O ALA* 3.0 28.7 - - + +
170O ALA* 4.3 4.5 - - - +
172O GLN* 3.0 17.9 + - + +
174O GLN* 1.3 78.2 - - - +
176O PHE* 1.3 61.2 + - + +
178O ALA* 2.9 4.7 + - - +
179O TYR* 2.8 63.9 + - + +
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Residues in contact with PHE 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M PHE* 3.6 65.7 - + + -
216M ARG* 5.8 0.7 + - - -
170O ALA 3.8 19.1 - - - -
171O ASN* 4.5 6.3 - - - -
172O GLN 3.8 13.0 - - - -
173O GLY* 2.8 13.3 + - - +
175O ILE* 1.3 74.6 - - + +
177O GLU* 1.3 61.4 + - - +
179O TYR* 3.2 22.8 + + + +
180O ASN* 3.2 23.7 + - - +
216O ARG* 3.6 54.5 - - + -
219O PHE* 5.6 0.3 - - - -
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Residues in contact with GLU 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171M ASN* 3.5 12.3 - - - +
172M GLN* 3.6 8.0 + - - -
173M GLY* 2.7 40.5 + - - +
173O GLY 3.2 3.4 + - - +
174O GLN* 3.6 9.8 - - - +
175O ILE 3.1 0.2 - - - -
176O PHE* 1.3 73.4 - - - +
178O ALA* 1.3 64.5 + - - +
180O ASN* 3.8 5.5 + - - +
181O MET* 3.0 30.5 + - - +
58P SER* 3.4 35.5 + - - -
59P GLU 4.2 0.3 + - - -
60P MET* 3.5 13.4 + - - +
61P GLY* 2.7 36.2 + - - -
88P GLN* 5.1 1.2 + - - -
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Residues in contact with ALA 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142O VAL* 4.1 28.3 - - + +
143O PRO* 4.4 10.5 - - + -
146O ALA* 4.6 7.0 - - + +
174O GLN 3.0 12.5 + - - +
175O ILE 2.9 8.8 + - - +
177O GLU* 1.3 75.8 - - - +
179O TYR* 1.3 69.1 + - - +
180O ASN 3.0 0.5 + - - -
181O MET* 3.1 8.2 + - - +
182O ALA* 2.9 22.0 + - - +
191O PHE* 4.1 11.0 - - + -
61P GLY* 5.2 1.5 - - - -
65P ILE* 5.4 2.0 - - + -
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Residues in contact with TYR 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165O TYR* 2.4 28.5 + - - -
170O ALA* 5.6 2.3 + - - +
175O ILE* 2.8 41.2 + - + +
176O PHE* 3.2 39.2 + + - +
178O ALA* 1.3 75.3 - - - +
180O ASN* 1.3 63.4 + - - +
182O ALA* 3.3 0.5 + - - +
183O ALA* 3.0 23.0 + - - +
191O PHE* 3.8 31.2 - + - -
216O ARG* 4.2 7.7 - - + +
217O GLY* 4.1 20.0 - - - +
219O PHE* 4.3 7.9 - - + -
220O ILE* 3.4 22.8 - - + +
252O LEU* 3.6 25.8 - - + +
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Residues in contact with ASN 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171M ASN* 3.4 38.3 - - + +
207M ALA 3.5 17.4 + - - -
208M ALA* 3.9 0.7 - - - -
209M ALA* 3.1 26.2 + - - +
210M SER 4.5 0.3 + - - -
216M ARG* 3.9 4.9 + - - +
176O PHE 3.2 12.2 + - - +
177O GLU* 4.0 6.5 + - - +
178O ALA 3.1 0.6 - - - -
179O TYR* 1.3 81.0 - - - +
181O MET* 1.3 59.9 + - - +
183O ALA* 3.6 2.1 + - - +
184O LEU* 3.0 27.6 + - - +
219O PHE* 3.8 18.2 - - + -
56P PRO* 4.1 11.5 - - - +
58P SER* 5.2 0.4 + - - -
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Residues in contact with MET 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177O GLU 3.0 29.2 + - - +
178O ALA* 3.1 4.1 + - - +
180O ASN* 1.3 77.2 - - - +
182O ALA* 1.3 60.7 + - - +
184O LEU* 3.1 6.2 + - + +
185O TRP* 2.7 72.4 + - + +
55P THR* 4.8 0.2 - - - -
56P PRO* 3.6 33.2 - - + -
58P SER* 4.1 9.2 - - - -
61P GLY* 3.8 30.5 - - - -
62P PHE* 3.8 15.5 - - - +
65P ILE* 3.8 15.7 - - + -
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Residues in contact with ALA 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O ALA* 4.6 4.0 - - + +
178O ALA 2.9 17.1 + - - +
179O TYR 3.6 1.1 - - - +
181O MET* 1.3 77.0 - - - +
183O ALA* 1.3 57.2 + - - +
186O LYS* 2.9 10.0 + - - -
187O LEU* 2.9 50.1 + - + +
189O CYS* 4.9 1.8 - - + -
191O PHE* 3.6 29.4 - - + -
250O PRO* 3.4 13.2 - - + +
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Residues in contact with ALA 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209M ALA* 3.6 9.9 - - + -
179O TYR 3.0 16.1 + - - +
180O ASN 3.8 0.4 - - - +
182O ALA* 1.3 79.0 - - - +
184O LEU* 1.3 62.4 + - - +
186O LYS* 3.2 20.4 + - - +
219O PHE* 3.6 27.8 - - + -
220O ILE* 4.1 8.5 - - + -
250O PRO* 3.5 13.3 - - + +
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Residues in contact with LEU 184 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206M ARG 3.8 24.0 - - - +
207M ALA* 3.9 24.9 - - - +
208M ALA 4.2 7.9 - - - +
209M ALA* 4.1 22.7 - - + +
180O ASN* 3.0 19.3 - - - +
181O MET* 3.4 5.4 - - + +
183O ALA* 1.3 79.9 - - - +
185O TRP* 1.3 87.6 + - + +
186O LYS* 3.3 9.9 + - - +
56P PRO* 4.3 12.1 - - + -
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Residues in contact with TRP 185 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O LEU* 4.7 11.9 - - + -
153O LYS* 2.9 34.9 + - - +
181O MET* 2.7 56.4 + - + +
184O LEU* 1.3 96.0 - - + +
186O LYS* 1.3 71.7 + - - +
187O LEU* 3.4 28.9 - - + -
26P LEU* 4.8 6.5 - - + -
53P ILE* 3.6 33.8 - - + +
54P ASP 3.6 15.8 + - - -
55P THR* 4.3 10.5 - - + -
56P PRO* 4.3 6.5 - - + -
65P ILE* 4.0 22.0 - - + -
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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