Contacts of the helix formed by residues 203 - 215 (chain A) in PDB entry 6CQT
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 SER 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY* 4.6 0.9 - - - -
202A GLU* 1.3 78.5 - - - +
204A ALA* 1.3 56.6 + - - -
206A ALA* 2.9 19.3 + - - +
207A ALA 2.9 10.7 + - - -
228A GLN 2.9 13.5 + - - -
229A SER 3.2 14.5 + - - -
230A GLY* 3.8 2.5 - - - -
236A TRP* 3.7 10.5 - - - -
447A HIS* 3.0 26.1 + - - -
607A VX 1.6 47.0 + - - +
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Residues in contact with ALA 204 (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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119A TYR 4.3 0.9 - - - -
120A GLY* 4.1 1.6 - - - -
121A GLY 4.1 4.0 - - - +
122A GLY* 3.6 15.9 - - - +
123A PHE* 3.6 32.9 - - + +
151A TYR* 4.7 2.7 - - - +
202A GLU 3.2 0.4 + - - -
203A SER* 1.3 79.6 + - - +
205A GLY* 1.3 57.2 + - - +
207A ALA* 3.6 3.0 - - - +
208A SER* 2.8 32.6 + - - -
236A TRP* 3.7 13.6 - - + -
607A VX 3.0 14.2 + - - +
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Residues in contact with GLY 205 (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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118A ILE* 3.3 30.0 - - - +
119A TYR 3.4 12.7 + - - -
201A GLY* 3.7 7.1 - - - -
202A GLU 2.8 8.8 + - - -
204A ALA* 1.3 77.0 - - - +
206A ALA* 1.3 59.2 + - - +
208A SER* 3.3 2.1 + - - -
209A VAL* 2.9 32.7 + - - +
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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
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201A GLY 3.4 19.7 - - - +
202A GLU 3.4 5.5 - - - +
203A SER 2.9 9.6 + - - +
205A GLY* 1.3 73.8 - - - +
207A ALA* 1.3 65.4 + - - +
209A VAL* 3.2 6.6 + - - +
210A GLY 3.0 18.4 + - - -
227A LEU* 3.3 15.7 - - - +
228A GLN 3.4 22.2 - - - +
230A GLY 3.4 21.8 - - - +
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Residues in contact with ALA 207 (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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123A PHE* 4.1 6.7 - - + -
203A SER 2.9 6.1 + - - -
204A ALA* 3.6 9.0 - - - +
206A ALA* 1.3 76.0 - - - +
208A SER* 1.3 57.3 + - - +
210A GLY 3.2 1.2 + - - -
211A MET* 2.9 34.4 + - + +
231A ALA 3.6 20.2 - - - +
232A PRO* 3.6 16.6 - - + +
236A TRP* 3.8 21.1 - - + -
237A ALA* 4.0 11.7 - - + -
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 4.0 4.9 - - - -
123A PHE* 3.4 15.1 - - - -
151A TYR* 4.6 0.7 + - - -
173A LEU* 4.0 7.2 - - - +
176A GLN* 3.1 39.1 + - - -
204A ALA 2.8 27.0 + - - -
205A GLY* 3.5 7.1 - - - -
206A ALA 3.2 0.4 - - - -
207A ALA* 1.3 70.3 - - - +
209A VAL* 1.3 65.8 + - - +
211A MET* 3.0 9.3 + - - +
212A HIS* 2.9 29.1 + - - -
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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
----------------------------------------------------------
118A ILE* 4.0 10.3 - - + +
199A LEU* 4.0 24.0 - - + -
200A PHE 4.0 7.4 - - - -
201A GLY 3.9 20.9 - - - +
205A GLY 2.9 19.7 + - - +
206A ALA* 3.5 9.0 - - - +
208A SER* 1.3 75.9 - - - +
210A GLY* 1.3 63.2 + - - +
212A HIS* 3.2 10.4 + - - +
213A LEU* 3.0 20.3 + - + +
222A PHE* 4.5 0.9 - - - -
225A ALA* 3.6 30.5 - - + -
226A VAL 4.1 5.4 - - - +
227A LEU* 4.0 11.7 - - + -
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Residues in contact with GLY 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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206A ALA 3.0 11.5 + - - -
207A ALA 3.2 3.8 + - - -
209A VAL* 1.3 76.7 - - - +
211A MET* 1.3 62.2 + - - +
213A LEU* 3.1 15.3 + - - +
214A LEU* 3.1 26.4 + - - +
227A LEU* 4.1 8.5 - - - -
232A PRO* 3.7 24.5 - - - -
414A LEU* 5.4 0.9 - - - -
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Residues in contact with MET 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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123A PHE* 4.4 1.6 - - + -
173A LEU* 3.8 14.8 - - + -
207A ALA* 2.9 25.2 + - + +
208A SER* 3.0 8.5 + - - +
210A GLY* 1.3 77.1 - - - +
212A HIS* 1.3 60.7 + - - +
214A LEU* 3.0 5.5 + - - +
215A SER* 3.0 25.6 + - - -
232A PRO* 3.8 20.2 - - + +
237A ALA* 3.4 32.5 - - + +
238A THR* 3.6 16.8 - - + -
301A PRO* 3.6 27.1 - - + -
307A PHE* 3.9 16.2 - - + -
308A LEU* 4.1 21.9 - - + +
312A PRO* 5.0 0.9 - - + -
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Residues in contact with HIS 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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118A ILE* 4.1 11.4 - - + -
173A LEU* 3.8 23.4 - - + +
176A GLN* 2.9 29.4 + - + +
177A ARG* 3.9 11.4 - - - -
180A LEU* 4.1 13.9 - - + +
199A LEU* 4.2 3.4 - - + -
208A SER 2.9 28.1 + - - -
209A VAL* 3.5 7.9 - - - +
211A MET* 1.3 75.8 - - - +
213A LEU* 1.3 62.6 + - - +
215A SER* 3.3 18.3 - - - +
218A SER* 2.8 38.3 + - - -
219A ARG* 3.6 8.1 + - - -
222A PHE* 3.8 15.9 - - + -
307A PHE* 3.8 11.2 - + - -
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Residues in contact with LEU 213 (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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209A VAL 3.0 12.0 + - - +
210A GLY* 3.1 20.2 + - - +
212A HIS* 1.3 76.9 - - - +
214A LEU* 1.3 70.4 + - + +
215A SER 3.6 0.3 + - - -
219A ARG* 3.7 29.9 - - - +
222A PHE* 3.7 28.2 - - + -
225A ALA* 3.9 18.4 - - + -
227A LEU* 4.6 7.0 - - + -
321A PHE* 5.0 8.5 - - + -
324A LEU* 3.8 38.1 - - + -
326A VAL* 4.4 6.3 - - + -
414A LEU* 5.8 3.4 - - + -
418A LEU* 4.7 9.2 - - + -
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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
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210A GLY* 3.1 20.1 + - - +
211A MET* 3.0 9.2 + - - +
213A LEU* 1.3 83.9 - - + +
215A SER* 1.3 58.0 + - - +
216A PRO* 3.6 8.6 - - - +
232A PRO* 3.8 23.1 - - + -
307A PHE 4.8 1.4 - - - +
308A LEU* 4.7 4.2 - - + -
309A SER* 5.6 1.4 + - - -
312A PRO* 4.2 14.6 - - + +
315A LEU* 3.7 44.9 - - + +
316A ILE* 4.0 20.2 - - + -
321A PHE* 3.9 31.6 - - + -
414A LEU* 5.6 1.1 - - + -
418A LEU* 5.8 0.2 - - + -
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Residues in contact with SER 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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177A ARG* 2.8 29.2 + - - -
211A MET 3.0 14.8 + - - -
212A HIS 3.3 4.4 + - - +
213A LEU 3.4 1.0 - - - -
214A LEU* 1.3 77.7 - - - +
216A PRO* 1.3 69.0 - - - +
217A PRO* 3.5 6.6 - - - +
218A SER* 2.9 14.9 + - - -
219A ARG* 3.0 10.8 + - - -
306A ASP 4.9 0.2 + - - -
307A PHE* 2.8 36.0 + - - -
308A LEU* 5.1 0.2 - - - -
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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