Contacts of the helix formed by residues 303 - 306 (chain A) in PDB entry 1HRN
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 ALA 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP 4.3 0.9 - - - +
12A THR* 5.7 0.2 - - - -
14A TYR* 3.6 32.8 - - + -
155A TYR* 3.6 21.7 - - + -
215A ASP 4.5 0.2 + - - -
218A ALA 2.7 13.5 + - - +
219A SER* 3.6 15.5 + - - +
302A GLY* 1.3 70.6 - - - -
304A THR* 1.3 61.9 + - - +
306A ILE* 4.4 0.4 - - - -
307A ARG* 3.0 36.8 + - - +
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Residues in contact with THR 304 (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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219A SER 3.4 11.8 + - - -
220A TYR* 3.5 1.4 - - - -
221A ILE* 3.8 23.6 - - + -
269A LEU* 3.9 14.6 - - + +
273A ASP* 3.6 25.9 - - - +
274A TYR* 4.0 10.5 - - + -
285A ALA* 2.7 41.3 + - + +
286A ILE* 4.9 0.4 - - + -
302A GLY 3.1 1.6 + - - -
303A ALA* 1.3 77.4 - - - +
305A PHE* 1.3 60.3 + - - +
307A ARG* 3.7 20.1 + - - +
308A LYS* 4.4 5.0 + - - +
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Residues in contact with PHE 305 (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 VAL* 5.5 0.2 - - + -
221A ILE* 3.8 24.6 - - + +
260A PHE* 4.0 20.4 - + + -
262A LEU* 3.8 12.1 - - + -
267A TYR* 3.5 40.6 - + + -
269A LEU* 4.6 5.6 - - + -
301A LEU* 4.0 27.1 - - + -
302A GLY 3.1 8.4 + - - +
304A THR* 1.3 76.7 - - - +
306A ILE* 1.3 65.4 + - + +
307A ARG 3.1 1.6 - - - -
308A LYS* 3.0 5.5 + - - +
309A PHE* 3.0 43.7 + + + -
322A PHE* 3.5 38.1 - + - -
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Residues in contact with ILE 306 (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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153A PHE* 4.3 22.4 - - + +
154A TYR* 5.9 0.2 - - - -
155A TYR* 3.6 37.0 + - + +
214A VAL* 4.7 8.7 - - + -
216A THR* 3.7 39.5 - - + +
301A LEU 4.2 10.1 - - - +
302A GLY 3.2 19.4 + - - +
305A PHE* 1.3 76.4 - - + +
307A ARG* 1.3 66.0 + - - +
308A LYS 3.1 0.3 + - - -
309A PHE 3.1 23.7 + - - +
310A TYR* 4.1 1.7 + - - -
311A THR* 4.0 15.3 - - - +
325A ALA* 4.7 1.6 - - - +
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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