Contacts of the helix formed by residues 203 - 218 (chain A) in PDB entry 4QNW
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 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A THR* 5.1 6.1 - - - +
199A ILE 3.2 17.5 + - - +
200A GLU 3.7 1.3 - - - +
201A ASN 3.2 0.8 - - - -
202A ARG* 1.3 74.5 - - - +
204A ARG* 1.3 65.2 + - - +
205A PHE 3.3 0.7 - - - -
206A ALA* 3.2 6.7 + - - +
207A VAL* 2.9 24.9 + - + +
244A GLN* 4.0 8.9 - - - +
247A TYR* 3.6 30.1 - - + -
248A LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ARG* 2.8 47.1 + - - +
195A TRP* 3.5 31.0 - - + -
200A GLU* 3.3 15.4 + - - +
201A ASN* 2.8 45.1 + - - +
203A ALA* 1.3 78.5 - - - +
205A PHE* 1.3 54.3 + - - +
207A VAL* 3.7 6.5 - - + -
208A GLU* 2.7 55.0 + - + +
406A GOL 5.0 4.1 + - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU* 5.1 0.9 - - + -
148A ILE* 3.8 36.1 - - + -
151A CYS* 3.8 27.4 - - + -
152A ILE* 4.3 7.4 - - + -
155A PHE* 4.8 1.1 - + - -
179A LEU* 4.0 13.0 - - + -
180A ILE* 3.6 36.8 - - + -
183A PHE* 3.4 57.0 - + + -
195A TRP* 3.6 11.1 - + + -
201A ASN 4.5 0.6 + - - -
202A ARG 4.1 1.6 + - - -
203A ALA 3.3 0.4 - - - -
204A ARG* 1.3 79.0 - - - +
206A ALA* 1.3 57.5 + - - +
208A GLU* 3.8 0.7 - - - +
209A VAL* 2.9 48.5 + - + +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 5.8 0.7 - - - +
180A ILE* 3.6 30.4 - - + +
184A THR* 4.3 5.6 + - - +
202A ARG 5.0 0.6 + - - -
203A ALA 3.2 8.6 + - - +
205A PHE* 1.3 78.4 - - - +
207A VAL* 1.3 63.0 + - - +
209A VAL* 4.0 4.8 - - - +
210A THR* 2.8 30.6 + - - +
224A VAL* 6.4 1.6 - - + -
226A LEU* 5.8 1.8 - - + -
248A LEU* 3.8 27.4 - - + -
252A MET* 4.4 3.6 - - + -
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ALA* 2.9 25.4 + - + +
204A ARG* 3.7 6.5 - - + +
206A ALA* 1.3 75.9 - - - +
208A GLU* 1.3 65.4 + - + +
210A THR* 3.2 3.3 + - - -
211A ARG* 2.8 51.0 + - + +
247A TYR* 5.2 2.0 - - + +
248A LEU* 4.1 6.1 - - + -
251A GLN* 3.7 31.6 - - + +
252A MET* 4.0 13.2 - - + -
254A ARG* 4.3 15.9 - - - +
255A LEU* 4.0 5.3 - - + +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.6 26.7 - - + +
195A TRP* 4.2 2.5 - - + -
204A ARG* 2.7 41.0 + - + +
205A PHE 4.0 0.7 - - - +
207A VAL* 1.3 73.5 - - + +
209A VAL* 1.3 66.2 + - - +
210A THR 3.1 0.9 - - - -
211A ARG* 3.0 45.1 + - - +
212A ALA* 3.0 25.1 + - - +
406A GOL 3.6 40.0 + - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.1 19.3 - - + +
155A PHE* 3.6 43.1 - - + -
172A ILE* 4.1 22.4 - - + -
180A ILE* 4.1 6.5 - - + -
205A PHE* 2.9 51.3 + - + +
206A ALA 4.0 3.4 - - - +
208A GLU* 1.3 76.1 - - - +
210A THR* 1.3 62.3 + - - +
212A ALA* 3.3 1.2 + - - +
213A VAL* 3.1 24.0 + - + +
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ILE* 3.7 22.4 - - + +
206A ALA* 2.8 23.0 + - - +
207A VAL 3.6 4.0 - - - -
209A VAL* 1.3 77.4 - - - +
211A ARG* 1.3 57.4 + - - +
213A VAL* 3.2 2.6 + - - +
214A ILE* 2.8 36.9 + - + +
222A VAL* 4.6 0.2 - - + -
224A VAL* 4.0 8.8 - - + +
252A MET* 3.7 17.3 - - - -
255A LEU* 3.6 19.3 - - + -
257A VAL* 3.6 31.4 - - + -
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Residues in contact with ARG 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 VAL* 2.8 28.7 + - - +
208A GLU* 3.0 42.7 + - - +
209A VAL 3.4 0.2 - - - -
210A THR* 1.3 77.6 - - - +
212A ALA* 1.3 56.1 + - - +
214A ILE* 3.4 10.2 + - - +
215A GLU* 3.0 27.0 + - - +
254A ARG* 5.5 2.9 - - - +
255A LEU* 3.9 23.8 - - + +
406A GOL 5.5 1.8 + - - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.4 42.4 - - + +
153A ALA* 5.4 0.4 - - - -
156A ALA* 3.5 18.6 - - + +
208A GLU 3.0 8.4 + - - +
209A VAL 3.8 3.1 - - - +
211A ARG* 1.3 73.0 - - - +
213A VAL* 1.3 66.5 + - - +
215A GLU* 3.3 8.7 + - - +
216A ALA 3.1 16.8 + - - -
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 5.2 2.0 - - + -
155A PHE* 3.8 39.5 - - + +
156A ALA* 4.0 0.9 - - - +
159A ALA* 3.8 9.6 - - + -
170A VAL* 3.7 30.5 - - + -
172A ILE* 4.0 16.2 - - + -
209A VAL* 3.1 21.0 + - + +
210A THR 3.8 3.1 - - - +
212A ALA* 1.3 77.5 - - + +
214A ILE* 1.4 61.5 + - - +
216A ALA* 3.0 9.0 + - - +
217A VAL* 2.9 22.2 + - + +
222A VAL* 3.7 17.5 - - + -
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 2.8 41.1 + - + +
211A ARG* 3.6 7.2 - - - +
213A VAL* 1.4 77.1 - - - +
215A GLU* 1.3 61.2 + - - +
218A GLY* 2.7 30.1 + - - +
219A ALA* 3.8 23.6 - - + +
222A VAL* 4.0 19.1 - - + -
255A LEU* 3.7 34.1 - - + +
257A VAL* 3.9 7.4 - - + -
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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
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211A ARG 3.0 16.4 + - - +
212A ALA* 3.7 9.0 - - - +
213A VAL 3.2 0.4 - - - -
214A ILE* 1.3 79.6 - - - +
216A ALA* 1.3 62.6 + - - +
218A GLY 4.7 0.5 + - - -
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Residues in contact with ALA 216 (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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156A ALA* 3.6 30.3 - - + +
159A ALA* 4.4 0.7 - - + -
160A ARG* 2.8 41.1 + - + +
212A ALA 3.1 13.2 + - - +
213A VAL* 3.0 10.9 + - - +
215A GLU* 1.3 79.3 - - - +
217A VAL* 1.3 62.4 + - + +
221A ARG* 5.0 0.2 + - - -
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Residues in contact with VAL 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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18A ARG* 4.6 1.6 + - - -
159A ALA* 3.6 34.3 - - + +
160A ARG* 4.1 5.4 - - - +
163A ILE* 3.6 24.9 - - + -
170A VAL* 4.5 4.5 - - + -
213A VAL* 2.9 23.5 + - + +
216A ALA* 1.3 83.4 - - + +
218A GLY* 1.3 63.1 + - - +
220A ASP* 4.4 1.0 - - - +
221A ARG* 2.9 44.9 + - + +
222A VAL* 3.7 20.6 - - + -
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Residues in contact with GLY 218 (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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18A ARG* 6.1 0.2 - - - -
214A ILE* 2.7 24.2 + - - -
215A GLU 4.7 0.8 + - - -
217A VAL* 1.3 75.7 - - - +
219A ALA* 1.3 67.1 + - - -
220A ASP* 3.2 7.2 - - - -
221A ARG* 3.0 13.6 + - - -
222A VAL* 3.3 12.8 - - - +
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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