Contacts of the helix formed by residues 216 - 224 (chain A) in PDB entry 2HAS
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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161A ASP* 2.9 14.3 + - - -
163A GLY* 3.2 4.6 - - - -
164A GLY* 1.3 73.3 - - - +
217A VAL* 1.3 58.2 + - - +
218A THR* 3.5 8.3 + - - -
219A LEU* 3.1 27.5 + - - +
220A GLU* 2.9 34.6 + - - +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A GLY 3.2 7.4 + - - +
216A SER* 1.3 71.6 + - - +
218A THR* 1.3 65.1 + - - +
220A GLU* 3.4 13.7 + - - +
221A LEU* 2.9 46.2 + - + +
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Residues in contact with THR 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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216A SER* 3.2 7.7 + - - -
217A VAL* 1.3 81.3 - - - +
219A LEU* 1.3 56.8 + - - +
221A LEU* 3.4 6.2 + - - +
222A SER* 3.0 30.6 + - - -
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Residues in contact with LEU 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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159A VAL* 5.0 4.9 - - + -
160A ASN 3.4 25.6 - - - +
161A ASP* 3.4 22.7 - - + +
216A SER* 3.1 22.9 + - - +
218A THR* 1.3 78.3 - - - +
220A GLU* 1.3 63.6 + - - +
222A SER* 2.7 22.7 + - - +
223A GLN* 3.0 42.6 + - + +
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Residues in contact with GLU 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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159A VAL* 5.9 3.6 - - + -
161A ASP* 2.7 29.4 - - + +
164A GLY* 3.2 17.9 - - - +
216A SER 2.9 25.4 + - - +
217A VAL* 3.7 15.7 - - - +
219A LEU* 1.3 77.3 - - - +
221A LEU* 1.3 55.8 + - + +
223A GLN* 4.9 1.3 - - - -
224A LEU* 2.6 40.8 + - - +
301A THR* 3.3 43.6 - - - +
302A LYS* 4.5 7.5 - - + +
304A GLY* 5.2 5.1 - - - -
305A HIS 4.5 4.2 - - - +
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 2.9 38.8 + - + +
218A THR* 3.9 5.4 - - - +
220A GLU* 1.3 75.1 - - + +
222A SER* 1.3 65.3 + - - +
223A GLN 3.4 0.2 + - - -
224A LEU* 3.4 28.3 - - + +
304A GLY* 4.7 11.9 - - - +
403A CYS* 5.0 19.1 - - - +
404A LEU* 4.6 13.0 - - + -
407A GLN* 3.5 43.0 - - + +
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Residues in contact with SER 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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218A THR* 3.0 18.1 + - - -
219A LEU* 2.7 26.7 + - - +
221A LEU* 1.3 76.7 - - - +
223A GLN* 1.3 72.0 + - - +
407A GLN* 4.8 4.9 - - - -
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Residues in contact with GLN 223 (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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159A VAL* 4.0 33.2 - - + +
219A LEU* 3.0 42.1 + - + +
220A GLU* 4.2 1.1 - - - +
222A SER* 1.3 87.1 - - - +
224A LEU* 1.3 73.8 + - - +
225A SER* 3.0 9.3 + - - +
413A LYS* 3.8 12.4 - - - -
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Residues in contact with LEU 224 (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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220A GLU* 2.6 26.2 + - - +
221A LEU* 3.4 24.9 - - + +
223A GLN* 1.3 74.3 - - - +
225A SER* 1.3 64.4 + - - +
226A MET 3.3 3.1 - - - -
227A LEU* 3.2 31.0 + - + -
228A PRO* 3.4 10.0 - - - +
302A LYS 3.4 8.0 + - - -
303A ALA 3.7 13.0 - - - +
304A GLY* 3.7 10.1 - - - -
404A LEU* 3.6 26.5 - - + -
407A GLN* 4.0 19.5 - - + -
408A PRO 5.9 0.4 - - - +
410A CYS* 4.6 6.1 - - + -
413A LYS* 3.8 23.3 - - + +
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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