Contacts of the helix formed by residues 216 - 222 (chain A) in PDB entry 3PU3
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A EDO 4.8 1.4 - - - -
16A EDO 3.4 17.2 + - - -
24A EDO 4.5 1.7 + - - -
212A VAL 2.9 17.3 + - - -
213A LYS 3.8 0.2 + - - -
214A LYS 3.5 1.4 - - - -
215A LEU* 1.3 76.0 - - - +
217A TRP* 1.3 64.2 + - - +
218A VAL* 3.3 8.7 + - - +
219A GLU* 3.2 22.2 + - - +
220A ASN* 3.1 26.0 + - - -
336A PHE* 4.0 18.8 - - - +
337A LEU 3.3 8.1 + - - -
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Residues in contact with TRP 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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5A EDO 3.6 17.7 - - - -
216A SER* 1.3 72.1 + - - +
218A VAL* 1.3 55.0 - - + +
220A ASN 3.2 0.3 + - - -
221A TYR* 2.7 55.6 + + + +
222A TRP 3.7 0.3 + - - -
337A LEU* 2.8 40.4 + - + +
338A HIS* 3.7 21.1 - - - -
339A SER* 2.9 24.4 + - - +
342A VAL* 3.9 18.6 - - + -
345A GLN* 3.7 18.4 - - - -
369A ALA* 4.2 17.0 - - + +
370A CYS* 4.1 24.0 - - - -
373A MET* 3.4 42.8 - - + -
402A LEU* 4.5 11.0 - - + -
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Residues in contact with VAL 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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12A GOL 5.2 0.9 - - - +
24A EDO 3.4 29.1 - - - +
216A SER* 3.3 7.4 + - - +
217A TRP* 1.3 77.2 - - + +
219A GLU* 1.3 62.4 + - - +
222A TRP* 3.0 51.2 + - + +
230A LYS* 4.2 7.0 - - + -
231A PRO* 3.8 41.7 - - + +
233A VAL* 6.3 1.1 - - + -
234A THR* 5.9 0.2 - - + -
337A LEU* 5.7 3.1 - - + +
363A PHE* 4.9 10.1 - - + -
369A ALA* 4.5 11.0 - - + -
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Residues in contact with GLU 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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16A EDO 2.9 31.4 + - - +
24A EDO 3.0 30.9 + - - -
213A LYS* 3.5 37.3 - - + +
216A SER* 3.2 16.9 + - - +
218A VAL* 1.3 80.5 - - - +
220A ASN* 1.3 64.6 + - - +
222A TRP 4.9 2.9 - - - +
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Residues in contact with ASN 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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5A EDO 2.5 29.2 + - - -
20A EDO 2.6 38.7 + - - +
213A LYS 3.8 10.1 - - - +
214A LYS* 2.9 19.5 + - - +
216A SER 3.1 17.8 + - - +
219A GLU* 1.3 82.9 - - - +
221A TYR* 1.3 75.2 + - + +
222A TRP 3.8 1.1 - - - +
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Residues in contact with TYR 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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5A EDO 3.0 13.8 + - - -
6A EDO 2.9 38.9 - - - -
10A EDO 2.6 37.5 + - - -
20A EDO 3.9 21.3 - - - -
217A TRP* 2.7 40.5 + + + +
220A ASN* 1.3 94.6 - - + +
222A TRP* 1.3 61.0 + - - +
223A PRO* 3.4 4.4 - - - +
369A ALA 6.0 0.2 - - - +
372A TYR* 3.6 16.8 - - + +
373A MET* 3.6 21.3 - - - -
376A HIS* 3.3 33.0 + + + -
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Residues in contact with TRP 222 (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 TRP 3.7 1.2 + - - -
218A VAL* 3.0 33.8 + - + +
219A GLU 4.9 2.9 - - - +
220A ASN 5.2 0.3 - - - -
221A TYR* 1.3 78.2 + - - +
223A PRO* 1.3 81.1 - - + +
224A ASP* 3.6 2.8 + - - +
226A ALA* 3.6 8.5 - - + +
228A LEU* 3.1 26.4 + - + -
229A ALA 3.4 18.4 - - - -
230A LYS* 3.6 33.7 + - + +
231A PRO* 3.7 24.7 - - + -
365A ASN* 3.7 15.9 - - + -
368A THR* 3.2 29.4 - - + -
369A ALA* 3.5 30.3 - - + -
372A TYR* 3.6 20.4 - + + -
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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