Contacts of the helix formed by residues 214 - 220 (chain A) in PDB entry 6TXA
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.6 8.0 - - - +
148A LYS 2.7 19.1 + - - -
149A GLN 3.3 18.6 + - - -
151A GLY 4.8 1.1 - - - -
164A ARG* 2.9 32.0 + - - +
210A HIS* 3.5 20.8 + - - -
211A GLY 3.0 15.7 + - - -
213A PHE* 1.3 74.3 - - - +
215A HIS* 1.3 64.0 + - - -
217A PHE* 3.3 19.9 + - - +
218A ASP* 3.9 3.1 + - - +
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Residues in contact with HIS 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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149A GLN 5.7 0.2 - - - -
164A ARG* 4.2 13.4 + - - -
210A HIS* 3.8 17.4 + + - -
213A PHE 3.0 1.8 + - - -
214A SER* 1.3 76.2 - - - +
216A MET* 1.3 60.4 + - - +
217A PHE 3.1 1.8 - - - -
218A ASP* 3.2 21.2 + - - -
219A GLY* 2.8 33.0 + - - -
220A ARG* 5.2 0.3 - - - +
233A HIS* 3.8 27.8 - + - -
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Residues in contact with MET 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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212A PRO 3.9 12.8 - - - +
213A PHE* 3.1 26.1 + - + +
215A HIS* 1.3 77.7 - - - +
217A PHE* 1.3 59.9 + - - +
220A ARG* 2.9 33.0 + - - +
221A PHE* 3.0 13.1 + - + +
383A ASP* 3.7 39.2 + - + +
386A ILE* 3.6 25.1 - - + -
387A THR* 3.2 25.8 - - - +
390A PHE* 3.6 36.6 - - + -
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Residues in contact with PHE 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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211A GLY* 3.7 17.0 - - - +
212A PRO* 3.4 38.0 + - + +
214A SER 3.3 10.1 + - - +
215A HIS 3.1 0.4 - - - -
216A MET* 1.3 82.3 - - + +
218A ASP* 1.3 59.8 + - - +
221A PHE* 3.5 28.4 + + + -
222A ILE* 3.0 51.3 + - + +
231A TRP* 3.9 14.1 - + - -
390A PHE* 4.9 6.1 - + - -
409A ILE* 3.9 22.2 - - + -
413A ILE* 3.8 19.1 - - + -
419A TYR* 4.0 8.1 - + - -
422A LEU* 3.7 19.1 - - + -
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Residues in contact with ASP 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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214A SER 3.9 3.0 + - - +
215A HIS* 3.2 31.1 + - - +
217A PHE* 1.3 78.7 - - - +
219A GLY* 1.3 67.9 + - - +
223A PRO* 3.4 20.2 - - - +
231A TRP* 3.5 39.3 - - + +
232A THR* 4.1 6.7 - - - -
233A HIS* 3.2 40.4 + - + +
234A GLU* 5.0 0.2 - - - +
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Residues in contact with GLY 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 HIS* 2.8 19.5 + - - -
218A ASP* 1.3 81.8 + - - +
220A ARG* 1.3 63.2 + - - +
223A PRO* 3.9 12.3 - - - +
470A ARG* 5.9 0.7 + - - -
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Residues in contact with ARG 220 (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 HIS 5.2 0.2 - - - +
216A MET* 2.9 18.6 + - - +
219A GLY* 1.3 82.3 - - - +
221A PHE* 1.3 62.4 + - - +
222A ILE 3.7 0.7 - - - -
223A PRO* 3.8 4.2 - - - +
224A LEU* 3.3 30.7 + - + +
375A GLN* 4.7 5.3 - - - +
380A ASN* 3.6 25.5 + - - +
383A ASP* 3.7 31.8 + - - +
384A THR* 3.0 29.4 - - - +
387A THR* 3.5 21.3 - - + +
501A ASP* 3.1 35.5 + - - -
503A ILE* 5.3 1.0 - - - +
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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