Contacts of the helix formed by residues 212 - 221 (chain F) in PDB entry 6XAV
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 ARG 212 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ARG* 4.3 9.0 - - - +
337E GLY* 3.5 21.9 + - - +
338E THR* 3.2 27.3 + - - +
339E GLY 3.5 15.4 + - - -
340E ASN* 4.8 6.9 - - - +
366E ARG* 5.9 6.0 - - - +
185F THR* 5.2 3.8 + - - -
211F GLU* 1.3 88.6 + - - +
213F PRO* 1.3 72.4 - - + +
214F GLU* 4.0 16.2 - - + +
215F GLU* 2.7 53.4 + - + +
216F VAL* 3.1 24.1 + - - +
232F PHE* 3.6 3.8 - - + -
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Residues in contact with PRO 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PRO* 6.2 2.2 - - + -
302E GLY* 4.6 7.6 - - - +
305E ARG* 4.2 25.8 - - - +
211F GLU 3.9 0.2 - - - +
212F ARG* 1.3 83.1 - - - +
214F GLU* 1.3 71.7 + - - +
216F VAL* 3.1 4.5 + - + +
217F THR* 3.0 30.4 + - - +
231F THR* 3.7 19.3 - - + +
232F PHE* 3.5 20.6 - - + -
233F ASP* 3.8 21.3 - - - +
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Residues in contact with GLU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E PRO* 5.4 7.2 - - + +
139E LEU* 5.3 8.4 - - - +
140E HIS* 4.3 21.7 - - + +
173E ARG* 2.5 47.9 + - - +
302E GLY 5.0 3.4 - - - +
304E ALA 3.8 9.7 - - - +
305E ARG* 4.1 13.3 + - - +
340E ASN* 4.7 9.2 - - - +
212F ARG* 4.0 7.3 - - + +
213F PRO* 1.3 90.0 - - - +
215F GLU* 1.3 62.8 + - + +
217F THR* 3.3 11.6 - - - +
218F GLU* 3.1 27.0 + - - +
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E HIS* 5.0 11.7 + - + +
340E ASN* 5.5 1.4 - - - +
366E ARG* 5.4 9.0 - - - +
185F THR* 4.3 26.2 + - + +
189F GLN* 6.3 0.4 - - - +
208F LEU* 4.9 3.3 - - + +
211F GLU* 5.5 4.7 - - + +
212F ARG* 2.7 59.6 + - + +
213F PRO 3.3 0.4 - - - -
214F GLU* 1.3 79.2 - - + +
216F VAL* 1.3 61.7 + - + +
218F GLU* 3.9 6.1 - - - +
219F MET* 2.9 31.4 + - + +
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Residues in contact with VAL 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F LEU* 3.9 15.7 - - + -
211F GLU* 4.2 10.1 - - + -
212F ARG 3.1 18.6 + - - +
213F PRO* 3.1 10.1 + - + +
215F GLU* 1.3 77.9 - - - +
217F THR* 1.3 60.8 + - - +
219F MET* 3.3 3.3 + - - +
220F GLN* 3.0 33.5 + - - +
227F VAL* 4.7 4.6 - - + +
229F ALA* 3.7 35.2 - - + +
230F SER 5.4 0.2 - - - +
231F THR* 3.8 19.3 - - + +
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Residues in contact with THR 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PRO* 4.0 39.3 + - + +
139E LEU* 6.0 0.9 - - + -
213F PRO 3.0 14.2 + - - +
214F GLU* 3.3 21.3 - - - +
216F VAL* 1.3 79.4 - - - +
218F GLU* 1.3 57.7 + - + +
220F GLN* 3.9 9.7 + - - -
221F ARG* 3.1 46.1 + - - +
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Residues in contact with GLU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LEU* 5.8 5.8 - - + +
140E HIS* 3.0 33.1 + - - -
367E LYS* 4.3 20.0 + - - +
189F GLN* 4.3 15.6 + - - +
214F GLU 3.1 16.7 + - - +
215F GLU* 4.0 6.7 - - - +
216F VAL 3.2 0.2 - - - -
217F THR* 1.3 77.6 - - + +
219F MET* 1.3 63.5 + - - +
220F GLN 3.3 0.4 - - - -
221F ARG* 3.8 3.1 - - - -
222F LEU* 3.1 40.3 + - + +
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Residues in contact with MET 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F THR* 5.2 2.0 - - + +
188F LEU* 3.7 24.0 - - + -
189F GLN* 3.7 35.2 - - + +
192F ALA* 4.3 13.9 - - - -
206F VAL* 4.0 24.0 - - + -
208F LEU* 4.6 11.0 - - + -
215F GLU* 2.9 20.1 + - + +
216F VAL 3.8 4.5 - - - +
218F GLU* 1.3 76.5 - - - +
220F GLN* 1.3 61.8 + - - +
222F LEU* 4.8 3.4 - - - -
223F VAL* 3.3 43.5 + - + +
227F VAL* 4.3 8.1 - - + -
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Residues in contact with GLN 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ASP* 5.8 4.6 + - - +
216F VAL* 3.0 21.7 + - + +
217F THR* 4.1 10.7 + - - +
218F GLU 3.3 0.2 - - - -
219F MET* 1.3 79.3 - - - +
221F ARG* 1.3 61.0 + - + +
222F LEU 3.2 4.9 + - - -
223F VAL* 3.6 14.6 - - - +
225F GLY 5.1 5.1 - - - +
227F VAL* 3.8 37.1 + - + +
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Residues in contact with ARG 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E THR* 4.7 24.6 + - - +
138E PRO 5.3 1.9 + - - -
139E LEU* 4.8 20.4 - - - +
308E GLU* 5.0 8.3 + - - -
217F THR* 3.1 35.7 + - - +
218F GLU* 3.6 4.0 + - - +
220F GLN* 1.3 83.4 - - + +
222F LEU* 1.3 57.9 + - - +
223F VAL 4.9 0.7 - - - -
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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