Contacts of the helix formed by residues 307 - 312 (chain A) in PDB entry 3SN6
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 LYS 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A TYR* 3.8 2.0 - - - -
301A VAL* 4.7 18.7 + - - +
304A GLY* 3.6 28.7 - - - +
305A LYS 3.7 4.1 + - - +
306A SER* 1.3 75.0 + - - +
308A ILE* 1.3 70.0 + - - +
309A GLU* 3.9 25.3 - - + +
310A ASP* 2.9 42.2 + - - +
311A TYR* 3.6 5.4 - - - -
315A PHE* 5.1 12.9 - - + -
333A ARG* 5.5 8.7 - - - +
336A ARG* 5.6 4.0 - - - +
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Residues in contact with ILE 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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253A TYR* 3.5 38.2 - - + +
266A LEU* 6.0 1.3 - - + -
297A LEU* 4.9 3.6 - - + -
301A VAL* 4.6 7.9 - - + -
306A SER 3.9 0.4 + - - -
307A LYS* 1.3 74.8 - - - +
309A GLU* 1.3 51.2 + - - +
311A TYR* 2.8 10.0 + - - -
312A PHE* 2.6 58.1 + - + -
315A PHE* 3.6 26.5 - - + -
337A ALA* 3.3 38.8 - - + +
340A PHE* 4.0 13.0 - - + -
341A ILE* 5.2 6.1 - - + -
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Residues in contact with GLU 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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307A LYS* 3.9 21.8 - - + +
308A ILE* 1.3 77.8 - - - +
310A ASP* 1.3 73.3 + - - +
312A PHE 3.2 15.9 - - - +
313A PRO* 3.1 29.0 - - + +
315A PHE* 4.2 7.9 - - + -
316A ALA* 3.6 32.8 - - + +
336A ARG* 5.5 2.1 + - - -
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Residues in contact with ASP 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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305A LYS 5.2 3.1 - - - +
306A SER* 5.6 0.3 - - - -
307A LYS* 2.9 34.3 + - - +
308A ILE 2.9 0.2 + - - -
309A GLU* 1.3 86.0 - - - +
311A TYR* 1.3 77.1 + - + +
313A PRO* 4.2 4.2 - - - +
63N SER* 3.8 20.8 - - - -
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Residues in contact with TYR 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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253A TYR* 3.4 30.7 - + - +
254A ASN* 4.1 29.1 + - + +
263A THR 5.2 3.1 - - - -
264A ASN* 3.4 32.3 + - + +
267A GLN* 5.5 0.2 - - - +
306A SER* 5.1 6.0 + - - -
307A LYS 3.6 16.8 - - - -
308A ILE 2.8 6.3 + - - -
310A ASP* 1.3 90.3 + - + +
312A PHE* 1.3 78.7 + - + +
313A PRO* 3.7 3.1 - - - -
62N GLY* 2.9 22.2 + - - -
63N SER* 4.4 12.3 - - - +
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Residues in contact with PHE 312 (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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253A TYR* 4.2 6.1 - - + -
264A ASN* 3.7 19.5 - - - -
266A LEU* 3.5 37.7 - - + -
267A GLN* 3.8 17.9 - - + -
270A LEU* 3.7 22.4 - - + -
308A ILE* 2.6 25.4 + - + +
309A GLU* 3.2 6.7 - - - -
311A TYR* 1.3 100.6 - - + +
313A PRO* 1.3 65.7 - - - +
314A GLU* 2.9 22.0 - - - +
315A PHE* 2.9 19.2 + - - +
340A PHE* 3.6 31.0 - + + -
344A GLU* 4.4 8.3 - - + -
62N GLY* 4.6 0.7 - - - -
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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