Contacts of the helix formed by residues 204 - 213 (chain A) in PDB entry 6MOL
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 THR 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A HIS* 3.3 4.6 + - - -
196A ASN* 4.3 19.1 - - + +
197A ALA 3.2 11.0 - - - +
198A VAL* 4.2 15.5 - - + -
202A GLY 4.5 2.9 - - - +
203A GLY* 1.3 75.2 - - - -
205A PRO* 1.3 69.1 - - - +
206A LEU* 3.6 11.5 + - - +
207A HIS* 2.8 47.5 + - - +
208A GLU* 3.2 7.1 + - - +
227A ASP 5.2 0.2 + - - -
230A ALA* 3.8 24.6 - - + +
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Residues in contact with PRO 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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173A LEU* 3.9 32.1 - - + +
174A HIS* 3.3 25.1 - - + +
177A ALA* 3.6 12.3 - - + +
194A ASP 4.4 2.9 - - - +
195A VAL 3.6 23.3 - - - +
197A ALA* 3.3 17.3 - - + +
204A THR* 1.3 86.8 - - - +
206A LEU* 1.3 54.5 + - - +
208A GLU* 3.5 1.4 + - + +
209A ALA* 3.0 30.0 + - - +
221A LEU* 3.5 14.8 - - + +
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Residues in contact with LEU 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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195A VAL 4.9 1.8 + - - +
196A ASN* 5.6 0.7 - - - +
204A THR* 3.1 11.3 + - - +
205A PRO* 1.3 76.5 - - - +
207A HIS* 1.3 64.5 + - - +
209A ALA* 4.4 0.2 - - - -
210A ALA* 3.2 24.3 + - + +
218A VAL* 3.8 40.2 - - + +
221A LEU* 3.7 19.1 - - + +
222A LEU* 3.8 22.9 - - + -
226A ALA* 4.0 13.5 - - + -
227A ASP 3.4 24.9 - - - +
228A VAL* 3.9 5.4 - - - -
238A PRO* 3.8 22.0 - - + +
254A LEU* 4.3 4.7 - - + -
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Residues in contact with HIS 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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202A GLY 4.4 0.9 - - - -
203A GLY* 3.8 9.4 - - - -
204A THR* 2.8 37.0 + - - +
206A LEU* 1.3 79.8 - - - +
208A GLU* 1.3 62.5 - - - +
210A ALA 3.5 0.7 + - - -
211A ARG* 3.0 29.2 + - - +
230A ALA* 3.2 40.6 + - + -
231A VAL 4.0 2.2 - - - -
232A ASP* 4.1 14.8 - - + -
236A GLY 2.6 27.9 + - - -
237A THR 3.6 3.8 - - - -
238A PRO* 3.3 24.4 - - + +
241A GLU* 4.1 20.0 - - + +
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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
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174A HIS* 4.0 20.9 - - + +
177A ALA 3.9 4.0 - - - +
178A ARG* 3.3 56.6 + - + +
199A ASP* 4.4 9.3 - - - +
203A GLY* 4.6 5.4 - - - -
204A THR 3.2 11.2 + - - +
205A PRO* 4.1 5.2 - - + +
207A HIS* 1.3 83.5 - - - +
209A ALA* 1.3 62.5 + - - +
211A ARG* 3.4 29.3 + - - +
212A ALA* 3.2 22.9 + - - +
241A GLU* 5.5 0.9 - - - +
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Residues in contact with ALA 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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177A ALA* 3.5 20.4 + - + +
205A PRO 3.0 18.6 + - - +
206A LEU 4.1 1.3 - - - +
208A GLU* 1.3 76.8 - - - +
210A ALA* 1.3 59.2 + - - +
211A ARG 3.2 0.3 + - - -
212A ALA* 3.3 2.6 + - - +
213A GLY 3.0 24.6 + - - -
214A HIS* 3.4 10.7 + - + +
217A ILE* 4.3 9.9 - - + -
218A VAL* 3.8 20.2 - - + -
221A LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 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 LEU* 3.2 17.6 + - + +
207A HIS 4.2 2.0 - - - +
209A ALA* 1.3 78.5 - - - +
211A ARG* 1.3 60.7 + - - +
212A ALA 3.4 0.2 - - - -
213A GLY 4.1 0.4 - - - -
218A VAL* 3.9 3.7 - - + +
238A PRO* 3.6 28.7 - - + +
241A GLU* 3.7 2.4 - - + +
242A ALA* 3.7 11.3 - - + +
247A HIS* 3.4 19.6 - - - -
250A ILE* 3.7 30.7 - - + +
254A LEU* 4.4 1.1 - - + -
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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 HIS 3.0 17.9 + - - +
208A GLU* 3.6 29.9 + - - +
209A ALA 3.1 0.2 - - - -
210A ALA* 1.3 78.9 - - - +
212A ALA* 1.3 58.8 + - - +
241A GLU* 3.4 45.7 + - + +
244A ARG* 3.8 26.1 - - - +
245A ALA* 3.9 10.5 - - + +
247A HIS* 3.6 8.8 + - - -
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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
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178A ARG* 3.9 11.9 - - + +
208A GLU 3.2 11.1 + - - +
211A ARG* 1.3 80.6 - - - +
213A GLY* 1.3 57.7 + - - +
214A HIS* 3.3 34.0 - - + +
247A HIS* 3.3 13.8 + - - -
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Residues in contact with GLY 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 ALA 3.0 5.5 + - - -
211A ARG 3.6 0.6 - - - -
212A ALA* 1.3 79.3 - - - +
214A HIS* 1.3 66.0 + - - +
215A LEU* 3.4 6.9 + - - +
216A GLU* 5.6 0.2 - - - +
247A HIS* 3.4 32.0 + - - +
250A ILE* 3.6 9.5 - - - +
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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