Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 3EWS
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ALA* 4.0 26.4 - - + +
61A LEU* 5.9 0.2 - - - +
169A SER* 3.3 2.5 - - - -
170A PRO* 1.3 91.4 - - + +
172A TYR* 1.3 59.8 + - - +
173A GLU* 3.7 14.8 + - - +
174A LEU* 3.2 26.6 + - + +
175A ALA* 2.8 26.7 + - - +
217A THR* 3.7 10.8 - - - -
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 1.3 72.5 - - - +
173A GLU* 1.3 72.4 + - - +
175A ALA* 3.1 5.4 + - + -
176A LEU* 2.8 65.5 + - + +
196A TYR* 3.8 17.9 - + - -
198A VAL* 3.4 37.9 - - + -
200A GLY* 6.0 2.7 - - - -
217A THR* 3.8 5.4 - - + +
368B MET* 3.2 35.5 - - + +
370B GLU* 3.5 18.4 + - - -
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.5 32.3 - - + +
171A THR* 3.2 16.3 + - - +
172A TYR* 1.3 91.9 + - - +
174A LEU* 1.3 60.8 + - - +
176A LEU* 3.5 15.0 + - + +
177A GLN* 3.4 24.9 + - - +
370A GLU* 6.1 1.8 - - - +
172B TYR* 5.2 7.4 + - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.3 18.6 - - + +
60A SER* 4.0 14.4 - - - +
61A LEU* 3.7 37.2 - - + +
64A LYS* 3.9 22.7 - - + +
169A SER* 3.8 10.3 + - - +
170A PRO* 3.9 28.5 - - + -
171A THR* 3.2 22.1 + - - +
173A GLU* 1.3 75.0 - - - +
175A ALA* 1.3 65.5 + - - +
176A LEU 3.1 0.2 - - - -
177A GLN* 3.0 15.4 + - - +
178A THR* 3.1 14.9 + - - -
242A ASP* 5.6 0.4 - - - +
243A GLU* 4.2 9.9 - - + +
246A VAL* 4.6 1.1 - - + -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.6 19.8 + - - -
171A THR 2.8 13.6 + - - +
172A TYR* 3.1 17.2 + - + +
174A LEU* 1.3 75.8 - - - +
176A LEU* 1.3 52.5 + - - +
178A THR* 3.3 4.3 + - - +
179A GLY* 2.7 32.4 + - - -
196A TYR* 3.7 18.9 - - + -
198A VAL* 4.8 3.4 - - + -
215A ILE* 4.0 16.7 - - + +
216A GLY* 4.7 6.1 - - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 2.8 55.1 + - + +
173A GLU* 3.6 17.0 - - + +
174A LEU 3.1 0.4 - - - -
175A ALA* 1.3 75.9 - - - +
177A GLN* 1.3 62.7 + - - +
179A GLY 3.7 0.7 - - - -
180A LYS* 2.9 26.7 + - - +
196A TYR* 3.5 32.7 + - + +
370B GLU* 5.4 13.2 - - + +
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Residues in contact with GLN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 3.7 15.3 - - + +
64A LYS* 4.1 35.7 - - + +
65A LEU* 3.4 31.0 - - - +
145A THR* 5.7 0.7 - - - -
173A GLU 3.4 16.0 + - - +
174A LEU* 3.0 9.9 + - - +
176A LEU* 1.3 79.9 + - - +
178A THR* 1.3 65.0 + - - +
180A LYS* 3.3 36.4 + - - +
181A VAL* 3.4 12.5 + - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 5.8 2.6 - - - +
145A THR* 4.6 7.5 + - + +
148A PHE* 4.0 27.7 - - + -
149A VAL* 4.3 5.2 - - + -
167A CYS* 4.3 11.3 - - - -
169A SER* 4.1 3.6 + - - -
174A LEU 3.1 11.7 + - - -
175A ALA* 3.6 6.7 - - - -
177A GLN* 1.3 71.7 - - - +
179A GLY* 1.3 67.3 - - - +
181A VAL* 3.0 19.0 + - - +
182A ILE* 3.1 29.0 + - + +
215A ILE* 4.5 8.5 - - + -
242A ASP* 3.6 19.8 + - - -
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 2.7 15.3 + - - -
176A LEU 3.7 1.1 - - - -
177A GLN 3.3 0.2 - - - -
178A THR* 1.3 73.6 - - - +
180A LYS* 1.3 61.5 + - - +
182A ILE* 3.5 2.3 + - - +
183A GLU* 3.1 31.4 + - - +
194A LEU* 3.8 3.6 - - - -
196A TYR* 3.3 24.5 - - - -
215A ILE* 3.5 16.8 - - - +
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU 2.9 13.9 + - - +
177A GLN* 3.3 31.4 - - - +
178A THR 3.1 0.4 - - - -
179A GLY* 1.3 77.9 - - - +
181A VAL* 1.3 63.6 + - + +
183A GLU* 3.5 14.5 + - - +
184A GLN* 3.2 31.4 + - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A MET* 4.4 14.8 - - + -
112A PHE* 6.1 0.7 - - + -
145A THR* 3.8 24.9 - - + -
146A ALA* 4.5 6.7 - - + -
149A VAL* 3.9 23.6 - - + -
177A GLN 3.5 14.6 - - - +
178A THR 3.0 6.0 + - - +
180A LYS* 1.3 75.4 - - + +
182A ILE* 1.3 60.0 + - - +
184A GLN* 3.2 9.3 + - - +
185A MET* 2.8 36.0 + - + +
602A ADP 5.7 2.0 - - - +
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL* 3.7 26.7 - - + -
152A MET* 4.8 9.4 - - + -
153A LEU* 4.5 5.6 - - + +
167A CYS* 6.0 0.2 - - + -
178A THR* 3.1 21.4 + - + +
179A GLY 3.8 5.2 - - - +
181A VAL* 1.3 72.9 - - - +
183A GLU* 1.3 65.3 + - - +
184A GLN 2.9 4.0 - - - -
186A GLY* 2.9 24.9 + - - -
192A LEU* 4.6 11.7 - - + +
194A LEU* 4.5 11.4 - - + -
213A ILE* 4.2 34.1 - - + -
215A ILE* 3.6 34.1 - - + -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLY 3.1 19.3 + - - +
180A LYS* 3.8 14.9 - - - +
181A VAL 3.4 0.2 - - - -
182A ILE* 1.3 79.7 - - + +
184A GLN* 1.3 58.9 + - - +
186A GLY 4.0 1.3 - - - -
187A LYS* 3.5 22.2 + - - +
192A LEU* 6.3 0.9 - - - -
194A LEU* 3.9 16.3 - - + +
196A TYR* 3.6 18.0 + - - -
371B GLN* 5.0 7.4 + - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY 4.4 5.5 - - - +
110A MET* 3.5 43.8 + - + +
180A LYS* 3.2 27.3 + - - +
181A VAL* 3.2 6.2 + - - +
182A ILE 2.9 0.4 - - - -
183A GLU* 1.3 78.2 - - - +
185A MET* 1.3 64.1 + - - +
186A GLY 3.3 0.4 + - - -
187A LYS* 3.6 31.5 - - - +
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Residues in contact with MET 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLN 4.7 2.6 - - - +
103A LEU* 4.2 9.7 - - + +
106A GLY* 3.4 20.3 - - - -
107A VAL* 4.0 20.6 - - + +
110A MET* 3.7 28.0 - - - -
112A PHE* 4.1 16.4 - - + -
146A ALA* 3.5 27.1 - - + +
149A VAL* 4.0 9.0 - - + -
150A LEU* 3.4 41.5 - - + -
153A LEU* 3.9 11.9 - - + -
181A VAL* 2.8 21.6 + - + +
184A GLN* 1.3 74.6 - - - +
186A GLY* 1.3 57.6 + - - +
187A LYS 3.3 2.1 + - - -
188A PHE 4.8 0.5 + - - -
189A TYR* 4.8 0.3 - - - -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.7 14.2 - - - +
182A ILE 2.9 14.8 + - - -
183A GLU* 4.0 4.7 - - - -
185A MET* 1.3 77.8 - - - +
187A LYS* 1.3 60.8 + - - -
188A PHE 3.1 3.4 - - - -
189A TYR* 3.2 39.6 + - - +
192A LEU* 4.1 7.9 - - - +
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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