Contacts of the helix formed by residues 302 - 311 (chain A) in PDB entry 5H1Y
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLY 4.3 0.4 + - - -
301A MET* 1.3 78.1 - - - +
303A VAL* 1.3 60.4 + - - +
304A LYS* 3.7 9.3 + - - +
305A GLU* 3.1 32.4 + - - +
306A GLN* 3.1 26.5 + - - +
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Residues in contact with VAL 303 (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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302A SER* 1.3 71.2 - - - +
304A LYS* 1.3 68.3 + - - +
306A GLN* 3.0 7.3 + - - +
307A MET* 2.9 26.9 + - + +
326A ASP* 6.2 0.2 - - - +
327A LEU* 5.3 10.8 - - + -
330A LYS* 6.0 5.2 - - + +
332A MET* 3.5 36.8 - - + -
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Residues in contact with LYS 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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302A SER* 3.8 8.5 - - - +
303A VAL* 1.3 81.0 - - - +
305A GLU* 1.3 57.8 + - - +
307A MET* 3.3 6.4 + - - +
308A GLU* 2.9 54.0 + - + +
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Residues in contact with GLU 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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300A GLY 4.6 0.9 - - - +
301A MET* 3.2 42.2 - - + +
302A SER* 3.1 22.5 + - - +
304A LYS* 1.3 76.8 - - - +
306A GLN* 1.3 67.1 + - - +
308A GLU* 3.1 26.4 + - - +
309A THR* 3.1 22.5 + - + +
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Residues in contact with GLN 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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296A LEU 3.2 20.3 - - - +
297A CYS* 3.3 29.2 - - - +
298A ILE 3.9 13.7 + - - -
301A MET* 3.6 21.6 + - + +
302A SER 3.1 18.3 + - - +
303A VAL* 3.0 10.4 + - - +
305A GLU* 1.3 75.9 - - - +
307A MET* 1.3 74.6 + - + +
309A THR* 3.0 26.9 + - - -
310A ILE* 3.5 11.3 + - - +
317A MET* 5.2 4.0 - - - +
323A ARG* 4.6 4.8 - - - +
327A LEU* 3.6 25.4 - - + +
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Residues in contact with MET 307 (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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303A VAL* 2.9 20.8 + - + +
304A LYS* 3.9 5.6 - - - +
306A GLN* 1.3 87.6 - - + +
308A GLU* 1.3 65.4 + - - +
310A ILE* 3.4 27.3 + - + +
311A ARG* 3.2 23.7 + - - +
327A LEU* 4.2 19.7 - - + -
332A MET* 3.6 53.8 - - + +
333A VAL* 4.7 1.1 - - + -
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Residues in contact with GLU 308 (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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304A LYS* 2.9 46.4 + - + +
305A GLU* 3.1 20.5 + - - +
307A MET* 1.3 77.6 - - - +
309A THR* 1.3 64.2 + - + +
311A ARG* 3.0 32.8 - - - +
312A HIS* 4.6 2.6 + - - -
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Residues in contact with THR 309 (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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293A ARG* 5.5 5.9 + - - +
294A CYS 5.7 1.3 - - - -
295A ALA* 3.7 20.1 - - - +
296A LEU 4.7 5.8 + - - +
301A MET* 4.5 16.6 - - + -
305A GLU* 3.1 20.8 + - + +
306A GLN* 3.0 13.9 + - - +
308A GLU* 1.3 76.0 - - + +
310A ILE* 1.3 67.6 + - - +
311A ARG 3.8 0.3 + - - -
312A HIS* 4.6 8.5 + - - +
313A GLY 4.7 5.2 - - - +
314A VAL* 5.4 0.7 - - - +
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Residues in contact with ILE 310 (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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254A LYS 3.1 4.9 - - - +
255A ARG* 4.4 5.4 - - - -
295A ALA* 3.9 18.8 - - + -
306A GLN* 3.7 6.1 - - - +
307A MET* 3.6 43.3 - - + +
308A GLU 3.2 0.2 - - - -
309A THR* 1.3 90.6 - - - +
311A ARG* 1.3 56.5 + - - +
312A HIS 3.0 6.1 - - - -
313A GLY* 2.8 25.8 + - - +
314A VAL* 4.1 20.1 - - + +
317A MET* 4.1 10.5 - - + -
332A MET 4.1 11.2 - - - +
333A VAL* 5.0 9.4 - - + -
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Residues in contact with ARG 311 (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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254A LYS* 2.6 47.7 - - - +
255A ARG* 5.7 0.2 - - - +
307A MET 3.2 12.1 + - - +
308A GLU* 3.0 31.4 - - - +
310A ILE* 1.3 77.6 - - - +
312A HIS* 1.3 95.0 + - - +
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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