Contacts of the helix formed by residues 172 - 185 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177Q GLU* 3.8 5.6 + - - +
57R ILE* 3.1 29.5 + - - +
58R SER* 4.4 2.0 - - - +
59R GLU* 3.6 7.1 + - - -
88R GLN* 3.4 26.7 + - - +
138S VAL* 3.3 24.7 + - + +
139S GLY* 4.0 4.5 - - - -
169S ALA* 3.1 20.5 + - - +
170S ALA 3.4 1.2 - - - -
171S ASN* 1.3 78.7 - - - +
173S GLY* 1.3 70.7 + - - +
174S GLN* 3.3 26.2 + - + +
175S ILE* 3.1 27.2 + - + +
176S PHE* 3.5 7.6 - - - -
60T MET* 5.8 0.2 - - - +
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Residues in contact with GLY 173 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Q GLY* 3.2 38.5 - - - -
177Q GLU* 2.8 23.3 + - - -
171S ASN 3.4 1.4 + - - -
172S GLN* 1.3 69.8 + - - +
174S GLN* 1.3 66.4 + - - +
176S PHE* 2.8 22.3 + - - +
177S GLU 3.4 6.1 + - - -
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Residues in contact with GLN 174 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Q GLY* 4.5 0.2 - - - -
88R GLN* 3.5 13.1 + - - -
138S VAL 3.7 1.2 + - - -
139S GLY 3.3 8.1 - - - +
140S ALA* 3.1 35.8 - - - +
143S PRO* 3.5 16.2 - - + +
172S GLN* 3.3 25.5 + - + +
173S GLY* 1.3 76.6 - - - +
175S ILE* 1.3 58.8 + - - +
177S GLU* 3.1 13.6 + - - +
178S ALA* 2.8 30.0 + - - +
60T MET* 3.3 42.9 - - + +
61T GLY 4.8 1.3 - - - +
91T ASP* 4.6 0.4 + - - -
92T GLN* 3.5 16.1 + - - -
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Residues in contact with ILE 175 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S GLY* 4.7 4.9 - - - +
142S VAL* 3.8 27.1 - - + -
165S TYR* 3.9 33.7 - - + -
169S ALA* 3.2 29.2 - - + +
170S ALA* 4.3 5.4 - - - +
172S GLN* 3.4 17.3 - - + +
173S GLY 2.8 1.8 + - - -
174S GLN* 1.3 77.9 - - - +
176S PHE* 1.3 62.3 + - + +
178S ALA* 3.1 8.5 + - - +
179S TYR* 2.9 58.8 + - + +
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Residues in contact with PHE 176 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Q ASN 5.4 0.4 - - - -
176Q PHE* 3.7 63.5 - + + -
218Q ASP* 6.0 1.1 - - + -
170S ALA 3.8 18.6 - - - -
171S ASN* 4.6 6.3 - - - -
172S GLN 3.5 16.8 - - - -
173S GLY 2.8 13.8 + - - +
175S ILE* 1.3 73.8 - - + +
177S GLU* 1.3 63.6 + - - +
179S TYR* 3.2 24.5 + + - +
180S ASN* 2.9 24.4 + - - +
216S ARG* 3.7 52.3 - - + -
219S PHE* 5.6 0.3 - - - -
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Residues in contact with GLU 177 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Q ASN 3.3 20.4 - - - +
172Q GLN* 3.7 6.2 + - - +
173Q GLY* 2.8 35.0 + - - +
173S GLY 3.4 2.2 + - - +
174S GLN* 3.1 12.0 + - - +
176S PHE* 1.3 76.4 - - + +
178S ALA* 1.3 62.1 + - - +
180S ASN* 3.5 6.6 + - - +
181S MET* 3.3 31.0 + - - +
58T SER* 3.1 32.5 + - - +
60T MET* 4.3 9.3 + - - +
61T GLY* 2.6 33.7 + - - -
88T GLN* 5.1 1.6 + - - -
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Residues in contact with ALA 178 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142S VAL* 4.0 24.7 - - + +
143S PRO* 4.1 20.0 - - + -
146S ALA* 4.4 10.8 - - + +
174S GLN 2.8 13.1 + - - +
175S ILE 3.5 7.6 - - - +
177S GLU* 1.3 75.1 - - - +
179S TYR* 1.3 64.6 + - - +
180S ASN 3.1 1.6 - - - -
181S MET* 3.5 7.0 + - - +
182S ALA* 3.0 28.0 + - - +
191S PHE* 4.0 3.9 - - + -
61T GLY* 5.2 0.6 - - - -
65T ILE* 5.3 0.9 - - + -
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Residues in contact with TYR 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165S TYR* 2.6 27.3 + - - -
170S ALA 5.8 0.2 + - - -
175S ILE* 2.9 37.3 + - + +
176S PHE* 3.5 36.6 - + - +
178S ALA* 1.3 75.3 - - - +
180S ASN* 1.3 58.5 + - - +
182S ALA* 4.2 2.7 - - - -
183S ALA* 3.1 25.3 + - - +
191S PHE* 3.8 38.6 - + + -
213S TYR 5.0 0.2 + - - -
216S ARG* 4.3 6.1 - - + +
217S GLY* 3.8 24.2 + - - +
219S PHE* 3.6 9.4 - + + -
220S ILE* 3.3 25.8 - - + +
252S LEU* 3.9 15.8 - - + +
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Residues in contact with ASN 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Q ASN* 3.4 29.8 - - + +
207Q ALA 3.1 21.0 + - - +
208Q ALA* 3.8 1.7 - - - -
209Q ALA* 3.1 31.4 + - - +
216Q ARG* 4.1 7.9 + - - +
176S PHE 2.9 16.8 + - - +
177S GLU* 3.7 8.3 + - - +
178S ALA 3.1 0.2 - - - -
179S TYR* 1.3 77.7 - - - +
181S MET* 1.3 60.3 + - - +
183S ALA 3.4 0.5 + - - -
184S LEU* 2.8 29.6 + - - +
219S PHE* 4.1 10.4 - - + -
56T PRO* 3.7 18.2 - - - +
58T SER* 4.9 0.6 + - - -
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Residues in contact with MET 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177S GLU 3.3 24.7 + - - +
178S ALA* 4.4 0.7 - - - +
180S ASN* 1.3 75.8 - - - +
182S ALA* 1.3 57.2 + - - +
184S LEU* 3.9 6.1 - - - -
185S TRP* 2.9 72.5 + - + +
187S LEU* 4.4 0.4 - - - -
55T THR* 4.7 0.2 - - - -
56T PRO* 3.4 34.1 - - + -
58T SER* 4.3 9.2 - - - +
61T GLY* 3.4 35.7 - - - -
62T PHE* 3.5 17.9 - - + +
65T ILE* 3.5 19.3 - - + -
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Residues in contact with ALA 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146S ALA* 5.0 1.3 - - + -
178S ALA 3.0 20.3 + - - +
179S TYR 3.7 4.3 - - - +
181S MET* 1.3 77.1 - - - +
183S ALA* 1.3 61.7 + - - +
186S LYS 3.2 2.9 + - - -
187S LEU* 2.9 48.9 + - + +
189S CYS* 4.9 1.3 - - + -
191S PHE* 3.7 27.8 - - + -
250S PRO* 3.2 12.2 - - + +
65T ILE* 5.5 0.4 - - - +
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Residues in contact with ALA 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209Q ALA* 3.9 6.7 - - + -
179S TYR 3.1 19.2 + - - +
182S ALA* 1.3 76.6 - - - +
184S LEU* 1.3 63.0 + - - +
186S LYS* 3.3 17.3 + - - +
219S PHE* 3.6 28.7 - - + +
220S ILE* 4.0 9.4 - - + -
250S PRO* 3.5 12.4 - - + +
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Residues in contact with LEU 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205Q GLU 4.0 13.5 - - - +
206Q ARG 3.6 16.4 - - - +
207Q ALA* 3.0 24.5 - - - +
208Q ALA 3.8 22.9 - - - +
209Q ALA* 3.8 11.8 - - - +
180S ASN 2.8 19.4 + - - +
181S MET* 3.3 6.3 + - - +
183S ALA* 1.3 78.2 - - - +
185S TRP* 1.3 79.6 + - + +
186S LYS* 5.5 3.0 - - - +
54T ASP 5.9 0.2 - - - +
56T PRO* 4.1 15.5 - - + -
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Residues in contact with TRP 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Q ARG 5.6 0.4 + - - -
150S LEU* 4.6 16.6 - - + -
153S LYS* 3.4 17.5 + - - +
181S MET* 2.9 59.6 + - + +
184S LEU* 1.3 98.6 - - + +
186S LYS* 1.3 75.3 + - - +
187S LEU* 3.6 18.9 - - + +
26T LEU* 4.9 5.2 - - + -
53T ILE* 3.7 30.3 - - + +
54T ASP 3.8 16.8 + - - -
55T THR* 4.2 9.2 - - + -
56T PRO* 4.2 5.2 - - + -
65T ILE* 3.9 22.2 - - + -
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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