Contacts of the helix formed by residues 213 - 217 (chain A) in PDB entry 3H44
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 HIS 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ASN* 2.9 25.2 + - + +
211A PRO 4.1 0.3 - - - +
212A LYS* 1.3 79.1 - - - +
214A PRO* 1.3 74.1 - - + +
215A PHE* 3.3 23.7 + - + +
216A SER* 3.0 28.9 + - - -
217A LYS* 5.3 0.5 - - - +
288A PHE* 4.1 15.7 - + + +
290A GLU* 2.4 43.2 + - + +
291A HIS 3.9 2.9 - - - -
292A PRO* 3.6 35.1 - - + -
370A PHE* 4.1 16.8 - + - -
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Residues in contact with PRO 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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97A LEU* 3.4 33.8 - - + +
212A LYS 3.7 4.9 - - - +
213A HIS* 1.3 94.0 - - + +
215A PHE* 1.3 59.2 + - - +
216A SER 3.0 0.2 - - - -
217A LYS* 3.0 40.6 + - + +
288A PHE* 3.3 34.5 - - + -
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Residues in contact with PHE 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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97A LEU* 3.8 13.9 - - + +
202A PHE* 5.7 0.4 - + - -
205A GLU* 3.9 18.6 - - - -
206A LYS* 3.0 82.6 + - + +
209A GLY* 5.8 0.7 - - - -
213A HIS* 3.3 21.9 + - + +
214A PRO* 1.3 76.7 - - - +
216A SER* 1.3 57.5 + - - +
217A LYS 3.1 4.5 + - - +
292A PRO* 3.5 21.5 - - + -
293A PHE* 4.5 9.2 - + - -
366A GLY* 5.3 2.9 - - - -
370A PHE* 3.5 29.6 - + + -
372A PHE* 3.7 24.7 - + - -
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Residues in contact with SER 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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203A GLN* 3.9 9.4 + - - -
206A LYS* 3.3 26.9 - - - +
207A ALA* 4.9 5.0 - - - +
210A ASN 3.8 13.2 - - - -
211A PRO* 3.1 25.5 + - - +
213A HIS* 3.0 17.8 + - - +
215A PHE* 1.3 79.5 - - - +
217A LYS* 1.3 61.3 + - - +
495A TRP* 5.4 3.1 + - - -
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Residues in contact with LYS 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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96A SER 3.9 15.0 - - - +
97A LEU* 2.8 27.1 + - + +
98A SER* 4.2 0.8 - - - +
99A ASP* 2.6 34.1 + - + +
101A PRO* 4.4 25.7 - - + +
104A ALA* 6.0 3.1 - - + -
203A GLN* 3.1 14.7 + - - +
206A LYS* 3.8 10.6 + - - +
213A HIS 5.3 0.4 - - - +
214A PRO* 3.0 32.2 + - + +
215A PHE 3.1 1.3 - - - +
216A SER* 1.3 80.3 - - - +
218A PHE* 1.3 65.5 + - - +
219A GLY* 3.7 3.7 + - - +
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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