Contacts of the helix formed by residues 171 - 186 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ALA* 3.7 29.5 + - + +
169B SER* 3.3 3.1 - - - -
170B PRO* 1.3 88.0 - - + +
172B TYR* 1.3 59.0 + - - +
173B GLU* 3.7 12.1 + - - +
174B LEU* 3.3 26.4 + - - +
175B ALA* 2.9 29.1 + - - +
217B THR* 3.5 12.4 - - - +
253B HIS* 6.0 0.4 - - + -
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 5.2 6.9 + - - -
368A MET* 4.2 18.1 - - - -
370A GLU* 4.7 6.4 + - - -
171B THR* 1.3 73.0 - - - +
173B GLU* 1.3 80.4 + - + +
175B ALA* 3.3 6.9 + - + +
176B LEU* 2.9 55.4 + - + +
196B TYR* 5.7 1.6 - + + -
198B VAL* 3.6 44.4 - - + -
199B ARG 5.4 2.2 - - - -
217B THR* 3.7 5.5 - - + +
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.6 31.8 - - + +
171B THR* 3.8 10.9 + - - +
172B TYR* 1.3 100.4 + - + +
174B LEU* 1.3 61.4 + - - +
176B LEU* 3.4 12.1 + - + +
177B GLN* 3.2 25.8 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 4.0 22.7 - - + +
60B SER* 3.8 16.8 - - - -
61B LEU* 3.9 16.2 - - + +
64B LYS* 3.9 21.7 - - + +
169B SER* 4.1 2.7 - - - -
170B PRO* 4.0 28.5 - - + -
171B THR* 3.3 23.0 + - - +
173B GLU* 1.3 74.4 - - - +
175B ALA* 1.3 65.6 + - - +
177B GLN* 3.0 14.6 + - - +
178B THR* 3.1 17.2 + - - -
243B GLU* 3.8 30.4 - - - +
246B VAL* 4.8 1.3 - - + -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.6 21.0 - - - -
171B THR 2.9 20.0 + - - +
172B TYR* 3.5 9.4 - - - +
174B LEU* 1.3 76.0 - - - +
176B LEU* 1.3 58.5 + - - +
178B THR* 3.6 2.5 + - - -
179B GLY 3.0 22.9 + - - -
196B TYR* 3.5 17.5 - - + -
198B VAL* 4.8 3.6 - - + -
215B ILE* 3.9 17.4 - - + +
216B GLY* 4.8 10.3 - - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A MET* 5.2 3.6 - - + -
370A GLU* 4.8 14.8 - - - +
172B TYR* 2.9 53.3 + - + +
173B GLU* 3.5 14.4 - - + +
174B LEU 3.2 0.4 - - - -
175B ALA* 1.3 74.5 - - - +
177B GLN* 1.3 68.4 - - - +
179B GLY* 3.8 1.4 - - - -
180B LYS* 3.2 25.8 + - - +
196B TYR* 3.9 32.6 + - + +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.7 18.6 - - + +
64B LYS* 4.3 31.7 - - + +
65B LEU* 3.7 30.3 - - - +
173B GLU 3.2 14.4 + - - +
174B LEU* 3.0 10.2 + - - +
176B LEU* 1.3 80.4 + - - +
178B THR* 1.3 66.8 + - - +
180B LYS* 3.0 32.5 + - - +
181B VAL* 3.5 9.7 + - - +
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS* 5.0 4.2 + - - +
145B THR* 4.7 7.0 + - + -
148B PHE* 3.8 33.4 - - + -
149B VAL* 4.4 6.7 - - + -
167B CYS* 4.4 4.9 - - - -
169B SER* 3.7 8.3 + - - -
174B LEU 3.1 9.5 + - - -
175B ALA 3.8 7.2 - - - -
177B GLN* 1.3 76.5 - - - +
179B GLY* 1.3 63.5 + - - +
181B VAL* 3.1 20.8 + - - +
182B ILE* 3.2 11.1 + - - +
215B ILE* 3.9 17.7 - - + -
242B ASP* 3.5 19.1 + - - -
243B GLU* 4.9 0.9 + - - -
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA 3.0 14.2 + - - -
176B LEU 3.8 0.2 - - - -
177B GLN 3.2 0.4 - - - -
178B THR* 1.3 76.6 - - - +
180B LYS* 1.3 57.0 + - - +
182B ILE* 3.4 3.5 + - - +
183B GLU* 3.0 33.4 + - - +
194B LEU* 3.7 12.0 - - - +
196B TYR* 3.2 25.6 - - - -
215B ILE* 4.1 6.7 - - - +
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.2 14.6 + - + +
177B GLN* 3.0 25.1 + - - +
179B GLY* 1.3 75.2 - - - +
181B VAL* 1.3 65.9 + - + +
183B GLU* 3.4 14.9 + - - +
184B GLN* 2.9 29.0 + - - +
196B TYR* 5.8 0.2 - - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 6.1 0.7 - - - +
110B MET* 4.2 9.6 - - + +
112B PHE* 6.2 0.2 - - + -
145B THR* 3.7 24.2 - - + -
146B ALA* 4.4 6.3 - - + -
149B VAL* 4.0 24.5 - - + -
177B GLN 3.6 11.0 - - - +
178B THR* 3.1 11.4 + - - +
180B LYS* 1.3 75.3 - - + +
182B ILE* 1.3 55.0 + - - +
184B GLN* 3.1 9.0 + - - +
185B MET* 2.7 51.7 + - + +
602B ADP 5.7 1.1 - - - +
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Residues in contact with ILE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.7 28.7 - - + -
152B MET* 4.6 9.9 - - + -
153B LEU* 4.3 10.6 - - + +
178B THR* 3.2 10.7 + - + +
179B GLY 3.5 6.5 - - - +
181B VAL* 1.3 76.0 - - - +
183B GLU* 1.3 64.0 + - - +
186B GLY* 2.9 24.4 + - - -
192B LEU* 4.9 6.2 - - + +
194B LEU* 4.3 15.9 - - + -
213B ILE* 4.0 35.2 - - + -
215B ILE* 3.2 36.6 - - + -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A GLN* 4.2 12.4 + - - +
179B GLY 3.0 20.3 + - - +
180B LYS* 4.0 17.7 - - - +
182B ILE* 1.3 76.5 - - + +
184B GLN* 1.3 60.9 + - - +
186B GLY* 3.9 1.4 - - - -
187B LYS* 3.4 22.9 + - - +
192B LEU* 6.4 0.7 - - - -
194B LEU* 3.8 16.7 - - + +
196B TYR* 3.1 26.0 + - - -
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLY 4.5 3.8 - - - +
109B ALA* 5.4 0.6 - - + -
110B MET* 3.2 46.3 + - + +
180B LYS* 2.9 20.0 + - - +
181B VAL* 3.6 5.8 - - - +
183B GLU* 1.3 77.1 - - - +
185B MET* 1.3 62.8 + - - +
187B LYS* 3.3 37.6 - - - +
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN 4.9 2.4 - - - +
103B LEU* 4.2 11.5 - - + +
106B GLY* 3.6 17.8 - - - -
107B VAL* 3.8 17.7 - - + +
110B MET* 3.4 30.1 - - + -
112B PHE* 4.6 6.1 - - + -
146B ALA* 3.8 22.9 - - + +
149B VAL* 3.6 26.2 - - + -
150B LEU* 3.7 32.1 - - + -
153B LEU* 3.9 10.8 - - + +
181B VAL* 2.7 28.7 + - + +
184B GLN* 1.3 74.2 - - - +
186B GLY* 1.3 58.6 + - - +
187B LYS 3.3 3.0 + - - -
188B PHE 4.9 0.5 + - - -
189B TYR* 5.6 0.2 - - - -
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.7 14.5 - - - +
182B ILE 2.9 16.1 + - - -
183B GLU* 3.9 4.0 - - - -
185B MET* 1.3 77.4 - - - +
187B LYS* 1.3 61.6 + - - +
188B PHE 3.2 2.9 - - - -
189B TYR* 3.1 32.8 + - - +
192B LEU* 4.2 13.0 - - - +
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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