Contacts of the helix formed by residues 206 - 219 (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 GLY 206 (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* 5.4 0.7 - - - +
204A GLY 3.3 1.4 - - - -
205A THR* 1.3 81.1 - - - +
207A LYS* 1.3 58.8 + - - +
208A THR 3.4 2.0 - - - -
209A LEU* 3.6 7.4 - - - +
210A LEU* 2.9 38.0 + - - +
328A VAL* 5.0 1.1 - - - -
1604A ADP 3.0 35.8 + - - -
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Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 3.4 47.2 - - + +
201A GLY 3.1 31.5 + - - +
202A PRO 3.3 13.8 + - - -
203A PRO* 4.0 4.2 - - - +
205A THR* 3.7 5.6 - - - +
206A GLY* 1.3 78.2 - - - +
208A THR* 1.3 62.9 + - - +
210A LEU* 3.3 8.0 - - - +
211A ALA* 3.2 17.7 + - - +
258A PHE* 4.6 1.3 - - - -
260A ASP* 5.2 5.1 + - - -
305A ALA* 3.9 19.5 - - + +
306A THR* 4.0 5.2 - - - +
307A ASN* 4.3 14.5 + - - +
328A VAL* 4.6 11.2 - - + +
1604A ADP 2.7 36.5 + - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LYS* 1.3 70.9 - - - +
209A LEU* 1.3 66.6 + - - +
211A ALA* 3.0 4.0 + - - +
212A ARG* 2.9 39.7 + - + +
224A HIS* 4.0 19.5 - - + +
258A PHE* 3.7 27.8 - - + -
260A ASP* 3.7 18.7 + - - -
1604A ADP 2.8 33.5 + - - +
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Residues in contact with LEU 209 (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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158A VAL* 4.0 17.7 - - + +
162A ASP* 3.5 10.3 - - + +
163A VAL* 3.5 25.1 - - + -
206A GLY* 3.6 9.6 - - - +
208A THR* 1.3 75.2 - - - +
210A LEU* 1.3 64.4 + - - +
212A ARG* 3.1 22.1 + - - +
213A ALA* 2.8 23.4 + - - +
343A HIS* 6.2 0.7 - - + -
1604A ADP 3.0 81.5 + - + +
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Residues in contact with LEU 210 (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* 4.9 5.2 - - + -
163A VAL* 4.1 28.7 - - + -
166A ALA* 5.1 4.9 - - + -
169A ALA* 4.2 14.6 - - + -
170A ILE* 4.4 14.4 - - + -
173A LEU* 4.1 23.6 - - + -
199A LEU* 4.3 12.6 - - + -
206A GLY 2.9 16.9 + - - +
207A LYS 3.3 10.8 - - - +
209A LEU* 1.3 76.4 - - - +
211A ALA* 1.3 65.4 + - - +
213A ALA* 2.8 14.7 + - - +
214A VAL* 3.0 17.5 + - - +
328A VAL* 3.7 31.2 - - + -
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Residues in contact with ALA 211 (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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207A LYS 3.2 3.1 + - - +
208A THR 3.0 9.0 + - - +
210A LEU* 1.3 79.6 - - - +
212A ARG* 1.3 63.1 + - - +
214A VAL* 3.3 11.3 + - - +
215A ALA 3.4 8.7 + - - -
222A PHE* 3.6 22.1 - - + -
256A ILE* 4.0 2.1 - - - +
258A PHE* 3.5 37.0 - - + -
303A MET* 3.7 24.8 - - + +
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Residues in contact with ARG 212 (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 SER* 5.8 0.4 + - - -
155A ASN* 4.0 15.2 - - - +
156A LYS* 2.9 42.1 + - - +
158A VAL* 3.4 31.7 + - + +
208A THR* 2.9 32.5 + - + +
209A LEU* 3.5 17.2 - - - +
211A ALA* 1.3 76.5 - - - +
213A ALA* 1.3 57.9 + - - +
215A ALA* 3.4 3.8 + - - +
216A GLY* 3.1 21.7 + - - -
222A PHE* 3.4 35.8 - - + -
224A HIS* 5.6 1.8 - - - -
1604A ADP 4.6 8.7 + - - -
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.2 15.1 - - + +
159A THR 3.7 17.3 - - - +
160A PHE* 3.6 24.9 - - + -
163A VAL* 4.3 6.3 - - + -
209A LEU 2.8 12.6 + - - +
210A LEU* 2.8 11.2 + - - +
212A ARG* 1.3 73.7 - - - +
214A VAL* 1.3 67.8 + - - +
217A GLU* 2.8 27.9 + - - +
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Residues in contact with VAL 214 (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* 4.2 7.2 - - + -
173A LEU* 4.0 41.3 - - + +
176A VAL* 4.3 9.2 - - + -
177A VAL* 4.0 17.0 - - + +
180A LEU* 3.7 14.4 - - + -
210A LEU 3.0 15.4 + - - +
211A ALA 3.3 5.4 + - - +
213A ALA* 1.3 77.3 - - - +
215A ALA* 1.3 62.5 + - - +
217A GLU* 3.2 2.3 + - - +
218A ALA* 3.0 23.0 + - - +
256A ILE* 2.6 34.3 - - + -
303A MET* 4.3 8.1 - - - -
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA 3.4 1.2 + - - -
212A ARG 3.6 8.7 - - - +
214A VAL* 1.3 79.9 - - - +
216A GLY* 1.3 56.6 + - - +
218A ALA* 3.4 1.3 + - - -
219A ASN* 2.8 23.6 + - - -
220A VAL* 3.0 30.9 + - - +
221A PRO 4.2 2.7 - - - +
222A PHE* 3.7 34.8 - - + -
256A ILE* 3.2 14.2 - - + +
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Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.0 43.9 + - - -
158A VAL 3.3 18.6 - - - -
159A THR* 4.3 1.6 - - - -
212A ARG 3.1 9.4 + - - -
215A ALA* 1.3 79.2 - - - +
217A GLU* 1.3 60.6 + - - +
219A ASN* 3.3 8.8 + - - -
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Residues in contact with GLU 217 (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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157A ARG* 4.7 4.1 + - - +
158A VAL 4.0 1.0 + - - -
159A THR* 3.0 18.7 + - - +
160A PHE* 2.6 58.2 + - + +
161A LYS* 4.9 9.7 + - - -
177A VAL* 4.0 20.8 - - + +
181A LYS* 4.3 8.3 - - - +
213A ALA 2.8 14.1 + - - +
214A VAL 3.7 3.4 - - - +
216A GLY* 1.3 79.0 - - - +
218A ALA* 1.3 57.3 + - - +
219A ASN* 3.2 1.6 + - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.0 8.1 - - + +
180A LEU* 3.5 36.3 - - + -
181A LYS* 3.7 28.1 - - + +
214A VAL 3.0 15.9 + - - +
215A ALA 4.1 1.6 - - - +
217A GLU* 1.3 75.7 - - - +
219A ASN* 1.3 74.5 + - - +
220A VAL* 3.5 8.7 + - + +
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Residues in contact with ASN 219 (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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157A ARG* 4.9 13.7 + - - +
215A ALA 2.8 9.1 + - - -
216A GLY* 3.3 9.1 + - - +
217A GLU 3.2 3.8 - - - +
218A ALA* 1.3 83.3 - - - +
220A VAL* 1.3 58.7 + - - +
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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