Contacts of the helix formed by residues 166 - 182 (chain A) in PDB entry 2CEA
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 ALA 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A VAL* 3.9 22.3 + - + +
164A GLY 3.3 3.2 - - - +
165A GLY* 1.3 80.6 - - - +
167A GLU* 1.3 61.4 + - - +
168A GLU* 3.2 9.4 - - - -
169A ALA* 3.1 14.5 + - + -
170A ILE* 2.9 31.7 + - + +
205A THR 5.9 0.7 - - - +
210A LEU* 5.1 7.4 - - + -
328A VAL* 5.3 11.2 - - + -
1604A ADP 5.2 2.0 - - - +
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Residues in contact with GLU 167 (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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165A GLY* 3.9 11.8 - - - +
166A ALA* 1.3 86.0 + - - +
168A GLU* 1.3 74.0 + - + +
170A ILE* 3.3 11.0 + - + +
171A GLU* 3.0 28.8 + - + +
334A LEU* 6.2 0.2 - - - +
335A GLY* 5.9 2.1 - - - -
338A LYS* 5.7 4.9 - - - +
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Residues in contact with GLU 168 (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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165A GLY 4.5 3.3 - - - +
166A ALA* 3.4 9.2 - - - -
167A GLU* 1.3 94.1 + - + +
169A ALA* 1.3 61.2 + - - +
171A GLU* 3.4 6.9 + - - +
172A GLU* 3.2 23.0 + - - +
442A ARG* 3.4 28.2 + - - +
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Residues in contact with ALA 169 (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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166A ALA* 3.1 14.9 + - + +
168A GLU* 1.3 80.0 + - - +
170A ILE* 1.3 65.8 + - - +
171A GLU 3.1 0.2 - - - -
172A GLU* 3.1 4.9 + - - +
173A LEU* 3.0 29.0 + - + +
210A LEU* 4.2 19.7 - - + -
326A ILE* 3.7 28.7 - - + +
327A VAL 4.8 4.7 - - - +
328A VAL* 4.6 5.8 - - + -
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Residues in contact with ILE 170 (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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160A PHE* 3.8 46.3 - - + +
163A VAL* 3.9 25.8 - - + +
166A ALA 2.9 22.8 + - - +
167A GLU* 3.3 10.3 + - + +
169A ALA* 1.3 75.9 - - - +
171A GLU* 1.3 66.6 + - - +
173A LEU* 2.9 9.4 + - - +
174A LYS* 2.9 48.7 + - - +
210A LEU* 4.4 11.7 - - + -
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Residues in contact with GLU 171 (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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167A GLU* 3.0 21.7 + - + +
168A GLU* 3.5 7.6 - - - +
169A ALA 3.1 0.2 - - - -
170A ILE* 1.3 78.7 - - + +
172A GLU* 1.3 61.4 + - + +
173A LEU 3.3 0.5 + - - -
174A LYS* 3.0 49.6 + - - +
175A GLU* 4.4 2.9 + - - +
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Residues in contact with GLU 172 (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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168A GLU 3.2 11.5 + - - +
169A ALA* 3.1 11.2 + - - +
171A GLU* 1.3 79.2 - - + +
173A LEU* 1.3 61.1 + - - +
174A LYS 3.6 0.2 + - - -
175A GLU* 3.4 25.3 + - - +
176A VAL* 4.5 3.1 + - - +
324A LYS* 3.0 35.3 + - - -
326A ILE* 4.2 21.1 - - + -
400B ARG* 5.5 8.5 + - - -
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Residues in contact with LEU 173 (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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160A PHE* 4.4 6.5 - - + -
169A ALA* 3.0 17.2 + - + +
170A ILE* 2.9 6.4 + - - +
172A GLU* 1.3 75.0 - - - +
174A LYS* 1.3 64.9 + - - +
175A GLU 3.2 2.5 - - - -
176A VAL* 3.0 21.1 + - + +
177A VAL* 3.0 16.0 + - - +
197A ILE* 4.4 15.5 - - + -
199A LEU* 5.0 0.9 - - + -
210A LEU* 4.1 36.8 - - + -
214A VAL* 4.0 30.3 - - + -
303A MET* 4.2 17.7 - - + -
326A ILE* 3.9 26.2 - - + -
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Residues in contact with LYS 174 (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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160A PHE* 3.8 21.1 - - + -
170A ILE* 2.9 31.6 + - + +
171A GLU* 3.0 39.8 + - - +
172A GLU 3.4 1.4 - - - -
173A LEU* 1.3 77.4 - - - +
175A GLU* 1.3 58.1 + - - +
177A VAL* 3.1 10.0 + - + +
178A GLU* 2.9 37.8 + - - +
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Residues in contact with GLU 175 (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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171A GLU 4.4 2.6 + - - +
172A GLU* 3.4 29.8 + - - +
173A LEU 3.2 0.6 - - - -
174A LYS* 1.3 76.6 - - - +
176A VAL* 1.3 67.7 + - + +
178A GLU* 3.2 21.1 + - - +
179A PHE* 3.0 22.5 + - - +
186A PHE* 4.0 7.9 - - + -
193A MET* 3.9 18.3 - - + +
324A LYS* 3.6 13.2 + - - -
379B LEU* 4.3 28.5 - - + +
383B ARG* 5.7 3.9 - - + +
400B ARG* 4.0 19.5 + - - -
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Residues in contact with VAL 176 (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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172A GLU 4.6 4.5 - - - +
173A LEU* 3.0 24.0 + - + +
175A GLU* 1.3 81.0 - - + +
177A VAL* 1.3 57.7 + - - +
179A PHE* 3.1 4.0 + - - +
180A LEU* 3.0 37.4 + - + +
193A MET* 3.5 22.4 - - + -
194A PRO* 5.2 1.3 - - + -
197A ILE* 3.7 27.1 - - + -
214A VAL* 4.3 10.5 - - + -
301A ILE* 3.3 31.2 - - + -
303A MET* 5.7 1.1 - - - -
324A LYS* 5.8 2.5 - - + -
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Residues in contact with VAL 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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160A PHE* 3.6 28.9 - - + -
173A LEU 3.0 17.4 + - - +
174A LYS* 3.1 8.9 + - + +
176A VAL* 1.3 74.5 - - - +
178A GLU* 1.3 66.6 + - + +
179A PHE 3.1 0.5 + - - -
180A LEU* 3.2 3.3 + - - +
181A LYS* 3.1 32.6 + - + +
214A VAL* 4.0 23.3 - - + +
217A GLU* 4.0 15.0 - - + -
218A ALA* 4.0 27.1 - - + +
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Residues in contact with GLU 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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174A LYS* 2.9 29.5 + - + +
175A GLU* 3.2 18.2 + - - +
177A VAL* 1.3 73.6 - - + +
179A PHE* 1.3 62.8 + - - +
181A LYS* 3.5 12.1 + - + +
182A ASP* 3.4 19.4 + - - +
186A PHE* 4.1 11.9 - - + -
382B ALA 6.0 0.2 - - - +
383B ARG* 3.3 41.8 - - - +
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Residues in contact with PHE 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 GLU 3.0 12.5 + - - +
176A VAL 3.3 7.4 - - - +
177A VAL 3.0 0.2 - - - -
178A GLU* 1.3 78.2 - - - +
180A LEU* 1.3 59.9 + - + +
182A ASP 3.1 0.7 + - - -
183A PRO* 2.9 51.5 - - + +
186A PHE* 3.6 32.5 - + + -
187A ASN* 4.2 12.3 - - - -
191A ALA 5.6 0.9 - - - -
193A MET* 3.7 31.2 - - + -
296A SER* 3.5 31.0 - - - -
299A GLY* 4.0 19.1 - - - -
300A ILE 4.8 0.2 - - - -
301A ILE* 3.4 35.7 - - + -
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Residues in contact with LEU 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 VAL* 3.0 24.3 + - + +
177A VAL 3.2 0.4 + - - +
179A PHE* 1.3 76.2 - - + +
181A LYS* 1.3 60.7 + - - +
182A ASP 3.2 0.9 + - - -
183A PRO* 3.9 8.7 - - - +
214A VAL* 3.7 12.6 - - + -
218A ALA* 3.5 23.6 - - + -
220A VAL* 4.2 12.8 - - + +
254A PRO* 3.9 18.0 - - + +
255A CYS* 4.1 17.7 - - - +
256A ILE* 3.5 34.1 - - + -
299A GLY* 3.3 30.5 - - - +
301A ILE* 4.3 11.9 - - + -
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Residues in contact with LYS 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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177A VAL* 3.1 31.1 + - + +
178A GLU* 3.8 9.4 - - - +
180A LEU* 1.3 74.7 - - - +
182A ASP* 1.3 63.5 + - + +
183A PRO* 4.2 0.4 - - - -
217A GLU 4.3 7.9 - - - +
218A ALA* 3.7 25.8 - - - +
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Residues in contact with ASP 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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178A GLU 3.4 9.4 + - - +
179A PHE 3.1 4.7 + - - +
180A LEU 3.1 1.2 + - - -
181A LYS* 1.3 85.0 - - + +
183A PRO* 1.3 71.2 - - - +
184A SER* 2.8 22.3 + - - -
185A LYS* 3.2 46.9 + - + +
186A PHE* 4.3 2.3 - - - -
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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