Contacts of the helix formed by residues 213 - 221 (chain A) in PDB entry 3B60
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 GLY 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLN 2.7 20.3 + - - -
210A MET 3.7 0.7 - - - -
212A LYS* 1.3 72.4 - - - +
214A HIS* 1.3 63.3 + - - +
215A LYS 3.4 2.7 - - - -
216A GLU* 3.1 6.7 + - - +
217A VAL* 2.8 30.8 + - - +
427B HIS* 3.2 21.0 + - - -
429B PHE* 4.2 9.4 - - - -
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Residues in contact with HIS 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 MET* 3.4 6.9 + - - +
211A LEU 2.9 18.0 + - - +
212A LYS 3.3 1.8 + - - -
213A GLY* 1.3 77.2 - - - +
215A LYS* 1.3 78.5 + - + +
217A VAL* 3.0 8.4 + - - +
218A LEU* 2.8 53.6 - - + +
109B MET* 3.6 29.5 + - - +
112B PRO* 3.9 18.2 - - + +
113B VAL 4.4 6.0 + - - -
116B PHE* 3.3 50.4 - + + -
392B PHE* 6.2 1.3 - + - -
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS 5.7 2.5 - - - +
214A HIS* 1.3 87.7 - - + +
216A GLU* 1.3 82.2 + - - +
218A LEU* 3.2 12.0 + - - +
219A ILE* 3.7 8.2 + - - +
479A VAL* 4.8 16.5 - - - +
116B PHE* 5.8 5.1 - - - +
117B ASP* 5.0 9.4 + - - -
392B PHE* 4.1 37.7 - - + -
393B TYR* 5.5 10.5 - - - -
423B SER* 5.9 4.3 - - - +
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Residues in contact with GLU 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 LYS 4.4 0.9 - - - +
213A GLY* 3.2 9.2 - - - +
215A LYS* 1.3 88.1 - - - +
217A VAL* 1.3 53.2 + - - +
218A LEU 2.4 17.0 + - - -
219A ILE* 2.9 10.6 + - - +
220A PHE* 2.6 32.6 + - + -
423B SER* 3.8 18.2 + - - -
427B HIS* 3.3 45.8 + - + +
429B PHE* 4.2 19.1 - - + -
493B ARG* 3.9 29.8 + - - +
497B ARG* 5.3 0.4 - - - +
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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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209A GLN 5.2 0.7 - - - +
210A MET* 4.2 12.3 - - + +
213A GLY* 2.8 32.4 + - - +
214A HIS* 3.0 8.3 + - - +
216A GLU* 1.3 69.8 - - - +
218A LEU* 1.3 66.2 + - + +
220A PHE* 3.1 23.7 - - + +
222A GLY 4.3 0.9 - - - -
223A GLN* 3.5 47.1 + - + +
226A GLU* 4.0 24.5 - - + +
109B MET* 4.4 9.9 - - + -
429B PHE* 4.6 4.9 - - + -
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Residues in contact with LEU 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 HIS* 2.8 59.7 - - + +
215A LYS 3.6 7.0 - - - +
216A GLU 2.4 15.8 + - - -
217A VAL* 1.3 77.3 - - + +
219A ILE* 1.3 65.1 + - - +
220A PHE 3.1 0.8 + - - -
221A GLY* 3.6 8.1 + - - -
223A GLN* 4.5 11.6 + - + +
109B MET* 5.1 3.4 - - + +
112B PRO* 4.9 6.1 - - + -
113B VAL 5.8 0.4 - - - +
392B PHE* 4.1 19.1 - - + -
416B ARG* 2.8 61.6 - - - +
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Residues in contact with ILE 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 LYS 4.1 4.0 - - - +
216A GLU* 2.9 16.4 + - - +
218A LEU* 1.3 72.3 - - + +
220A PHE* 1.3 74.9 - - - +
221A GLY* 3.2 1.7 + - - -
390B THR* 4.7 17.5 - - + -
392B PHE* 4.0 27.1 - - + -
416B ARG* 3.9 27.3 - - + +
417B ASN* 5.4 1.4 - - - -
419B VAL* 4.6 11.7 - - + +
420B ALA* 5.2 0.2 - - - -
421B LEU* 3.5 40.4 - - + +
441B ARG* 4.2 3.8 - - - +
493B ARG* 5.6 3.4 - - - +
497B ARG* 3.8 29.4 + - - +
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Residues in contact with PHE 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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216A GLU* 2.6 26.4 + - + +
217A VAL* 3.1 24.9 - - + -
219A ILE* 1.3 78.8 - - - +
221A GLY* 1.3 51.1 + - - +
222A GLY* 4.1 20.0 - - - -
225A VAL* 5.7 2.0 - - + -
226A GLU* 4.0 13.0 - - - -
429B PHE* 2.8 37.5 - + - -
436B ASN 5.3 1.1 - - - -
439B TYR* 2.8 56.1 - + + -
440B ALA* 4.8 0.2 - - - -
441B ARG* 2.5 31.3 + - - +
443B GLU* 4.6 2.9 - - + -
493B ARG* 5.3 9.2 - - - -
497B ARG* 2.7 30.8 + - - +
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Residues in contact with GLY 221 (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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217A VAL 3.9 0.4 + - - -
218A LEU 3.6 8.1 + - - -
219A ILE 3.2 4.2 + - - -
220A PHE* 1.3 68.5 - - - +
222A GLY* 1.3 58.3 + - - +
223A GLN* 3.4 9.0 - - - -
224A GLU* 4.4 0.6 - - - +
417B ASN* 6.5 1.1 - - - -
441B ARG* 2.2 67.0 + - - -
443B GLU* 3.6 5.3 - - - +
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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