Contacts of the helix formed by residues 208 - 227 (chain A) in PDB entry 4AS7
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 ASP 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.0 23.8 + - - +
128A GLU* 3.7 1.7 - - - +
206A ASN* 3.1 4.7 + - + +
207A LYS* 1.3 79.6 - - - +
209A GLU* 1.3 62.7 + - - +
211A TYR* 3.3 18.5 + - - +
212A GLN* 3.3 12.1 + - - +
1369A CD 2.4 29.5 - - - -
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR 5.4 0.2 - - - -
204A VAL* 4.0 7.4 - - + -
205A HIS* 3.0 10.5 + - - +
206A ASN* 2.8 49.7 + - + +
208A ASP* 1.3 76.3 - - + +
210A VAL* 1.3 62.7 + - - +
211A TYR 3.1 0.5 + - - -
212A GLN* 3.2 14.2 + - - +
213A ILE* 3.1 30.3 + - + +
1372A CD 2.2 30.8 - - - -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 3.8 26.5 - - + -
140A LEU* 3.4 41.7 - - + -
144A PHE* 5.4 1.3 - - + -
158A VAL* 5.3 3.1 - - + -
204A VAL* 3.7 28.6 - - + +
207A LYS* 3.0 17.4 + - + +
209A GLU* 1.3 76.6 - - - +
211A TYR* 1.3 60.3 + - - +
213A ILE* 4.2 7.9 - - + -
214A LEU* 2.9 35.9 + - + +
1375A 6LX 4.2 11.9 - - + -
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Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 2.5 35.3 + - - -
127A TRP* 4.0 27.1 - + + +
208A ASP 3.3 12.8 + - - +
209A GLU 3.1 0.8 - - - -
210A VAL* 1.3 83.6 - - - +
212A GLN* 1.3 72.8 + - - +
215A GLU* 2.8 58.4 + - + +
1375A 6LX 3.4 58.6 - + + +
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Residues in contact with GLN 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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208A ASP* 3.3 15.4 + - - +
209A GLU* 3.2 14.0 + - - +
211A TYR* 1.3 95.7 - - - +
213A ILE* 1.3 67.9 + - - +
215A GLU* 3.7 13.4 - - - +
216A LYS* 2.8 52.0 + - + +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.4 11.9 - - + -
172A LEU* 4.0 28.1 - - + +
202A ILE* 3.7 31.2 - - + -
203A THR 4.7 2.5 - - - +
204A VAL* 3.9 25.1 - - + -
209A GLU* 3.1 23.5 + - + +
210A VAL* 3.7 9.0 - - + +
212A GLN* 1.3 78.9 - - - +
214A LEU* 1.3 63.8 + - + +
216A LYS* 3.5 15.8 + - - +
217A GLY* 3.1 20.6 + - - -
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.8 20.6 - - + -
140A LEU* 4.5 7.0 - - + -
158A VAL* 6.0 0.9 - - + -
160A LEU* 4.3 11.9 - - + -
172A LEU* 4.4 10.3 - - + -
210A VAL* 2.9 19.0 + - + +
213A ILE* 1.3 83.5 - - + +
215A GLU* 1.3 61.7 + - - +
217A GLY* 3.5 1.3 - - - +
218A ALA* 2.9 22.0 + - - +
239A PHE* 4.3 18.8 - - + -
1375A 6LX 3.2 84.2 - - + -
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 5.5 1.4 + - - -
211A TYR* 2.8 42.3 + - + +
212A GLN* 3.1 13.4 + - - +
214A LEU* 1.3 74.6 - - - +
216A LYS* 1.3 66.6 + - + +
218A ALA* 3.3 5.4 + - + +
219A ALA* 3.2 20.1 + - - +
1375A 6LX 3.8 21.6 - - + +
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU 4.8 1.1 - - - -
174A PRO* 5.5 13.9 - - + -
212A GLN* 2.8 46.7 + - - +
213A ILE* 3.7 14.6 - - - +
215A GLU* 1.3 74.5 - - + +
217A GLY* 1.3 66.4 + - - +
219A ALA* 3.1 7.4 + - - +
220A LYS* 2.9 24.6 + - - +
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Residues in contact with GLY 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.6 24.0 + - - +
172A LEU* 4.4 7.2 - - - +
213A ILE 3.1 14.7 + - - -
214A LEU* 3.3 4.7 + - - -
215A GLU 3.2 0.6 - - - -
216A LYS* 1.3 76.9 - - - +
218A ALA* 1.3 56.5 + - - +
220A LYS* 3.4 2.9 + - - +
221A ARG* 2.9 28.1 + - - +
1375A 6LX 3.4 14.7 - - - +
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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
----------------------------------------------------------
214A LEU 2.9 16.9 + - - +
215A GLU* 3.3 8.5 + - - +
216A LYS 3.2 0.4 - - - -
217A GLY* 1.3 73.4 - - - +
219A ALA* 1.3 60.1 + - - +
221A ARG* 3.0 12.5 + - - +
222A THR* 2.8 34.0 + - - +
1375A 6LX 3.6 33.1 - - + +
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Residues in contact with ALA 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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215A GLU 3.2 10.7 + - - +
216A LYS* 3.1 10.4 + - - +
218A ALA* 1.3 73.1 - - - +
220A LYS* 1.3 68.5 + - - +
222A THR* 3.2 8.6 + - - +
223A THR* 3.0 27.5 + - - -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP 3.0 25.2 + - - -
171A LEU* 3.7 26.5 - - + +
173A ASN* 2.2 41.8 + - - +
174A PRO* 5.3 3.6 - - + +
176A SER* 3.2 22.1 - - - -
177A ASP* 4.1 9.6 - - - +
178A VAL* 4.1 25.1 - - + +
216A LYS 2.9 17.1 + - - +
217A GLY 3.7 4.0 - - - +
219A ALA* 1.3 76.8 - - - +
221A ARG* 1.3 61.5 + - - +
223A THR* 3.4 7.5 - - - +
224A ALA* 3.2 20.8 + - - +
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 5.0 3.0 + - - +
116A GLU* 2.8 42.6 + - - -
160A LEU* 5.2 0.4 - - - +
162A GLU* 3.8 23.9 + - - +
171A LEU* 3.9 18.6 - - + +
217A GLY 2.9 13.1 + - - +
218A ALA* 3.3 13.3 + - - +
219A ALA 3.0 0.4 - - - -
220A LYS* 1.3 76.5 - - - +
222A THR* 1.3 64.4 + - - +
224A ALA* 3.2 9.3 + - - +
225A ALA* 3.2 19.9 + - - +
231A TYR* 4.2 8.0 - - + -
232A SER* 5.5 7.2 - - - -
237A SER* 4.8 11.3 + - - -
265A ASP* 5.6 1.0 + - - -
1375A 6LX 3.4 42.8 + - - +
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Residues in contact with THR 222 (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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218A ALA* 2.8 19.9 + - - +
219A ALA* 3.6 8.7 - - - +
221A ARG* 1.3 71.5 - - - +
223A THR* 1.3 67.1 + - - +
225A ALA* 3.1 17.9 + - - +
226A THR* 3.3 18.9 + - + +
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Residues in contact with THR 223 (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 VAL* 3.7 36.5 - - + +
219A ALA 3.0 12.3 + - - -
220A LYS* 3.4 12.2 - - - -
222A THR* 1.3 78.9 - - - +
224A ALA* 1.3 63.4 + - - +
226A THR* 2.6 31.4 + - - +
227A LEU* 3.4 11.1 + - + +
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Residues in contact with ALA 224 (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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169A PHE* 6.5 0.2 - - + -
171A LEU* 5.1 4.5 - - + -
178A VAL* 6.0 3.4 - - + -
220A LYS 3.2 10.6 + - - +
221A ARG* 3.2 13.4 + - - +
223A THR* 1.3 80.0 - - - +
225A ALA* 1.3 57.6 + - - +
227A LEU* 2.6 34.4 - - - +
228A MET* 3.4 15.6 + - + +
231A TYR* 3.8 29.6 - - + +
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Residues in contact with ALA 225 (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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221A ARG 3.2 8.0 + - - +
222A THR* 3.1 12.7 + - - +
223A THR 3.1 1.0 + - - -
224A ALA* 1.3 78.0 - - - +
226A THR* 1.3 64.1 + - + +
228A MET 3.2 17.7 - - - +
231A TYR* 3.6 27.6 + - + +
232A SER* 5.4 2.9 - - - -
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 3.4 21.8 - - + +
223A THR* 2.6 23.1 + - - +
225A ALA* 1.3 76.0 - - + +
227A LEU* 1.3 72.2 + - - +
228A MET 4.2 0.2 + - - -
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A VAL* 4.5 21.1 - - + -
179A SER* 4.6 14.1 - - - +
223A THR* 3.5 14.8 - - + +
224A ALA* 2.6 14.8 - - - +
226A THR* 1.3 95.0 - - - +
228A MET* 1.3 79.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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