Contacts of the helix formed by residues 295 - 306 (chain A) in PDB entry 3N6J
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 ASN 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A TYR* 3.5 29.9 - - + +
100A PHE* 5.5 2.4 - - - -
293A ALA 4.4 0.2 - - - -
294A THR* 1.3 89.9 + - - +
296A TRP* 1.3 59.2 + - + +
297A ARG* 2.8 13.8 + - - +
298A GLU* 2.8 41.5 + - - +
299A MSE 2.8 27.4 + - - +
318A TRP* 3.3 15.8 - - - -
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Residues in contact with TRP 296 (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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295A ASN* 1.3 73.7 - - + +
297A ARG* 1.3 68.0 + - - +
299A MSE 3.7 13.5 - - + -
300A CYS 3.2 5.7 + - - -
318A TRP* 4.0 18.6 - + - -
322A GLY* 4.1 4.3 + - - -
325A ARG* 3.4 43.3 - - + +
326A VAL* 3.5 42.6 - - + -
329A LEU* 3.7 26.0 - - + -
329B LEU* 4.4 15.9 - - + -
332B GLU* 3.3 46.4 + - + -
333B TRP* 3.0 39.9 + - - +
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Residues in contact with ARG 297 (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 TYR* 3.4 56.2 + - + +
295A ASN* 2.8 13.2 + - - +
296A TRP* 1.3 76.4 - - - +
298A GLU* 1.3 64.7 + - + +
300A CYS* 3.4 10.3 - - - +
301A HIS* 3.3 29.4 + - + +
332B GLU* 4.2 14.6 + - - +
333B TRP* 5.9 0.2 - - - +
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Residues in contact with GLU 298 (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 TYR* 5.8 1.7 - - + -
100A PHE* 3.6 22.7 - - - -
273A ARG* 3.3 40.7 + - - +
291A MSE 5.1 0.4 - - - +
292A ILE 3.8 5.9 - - - +
293A ALA* 3.6 6.3 - - - -
294A THR* 2.5 47.3 + - - +
295A ASN* 2.8 26.1 + - - +
297A ARG* 1.3 75.0 - - + +
299A MSE 1.3 63.6 + - - +
300A CYS 3.1 0.7 + - - -
301A HIS* 3.2 7.9 + - - -
302A ALA* 3.2 19.1 + - - +
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Residues in contact with MSE 299 (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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289A THR* 5.9 0.2 - - + -
293A ALA* 4.0 22.4 - - + +
295A ASN 2.8 23.0 + - - +
296A TRP* 3.4 26.9 + - + +
298A GLU* 1.3 71.6 - - - +
300A CYS* 1.3 61.9 + - - +
302A ALA* 3.5 4.4 + - - +
303A ILE* 3.2 48.6 + - + +
308A VAL* 5.1 1.6 - - - -
311A PRO* 3.9 30.5 - - + -
312A LEU 6.2 0.7 - - - +
313A ALA* 6.0 0.4 - - + -
318A TRP* 3.5 29.6 - - + -
326A VAL* 4.4 11.2 - - + -
329A LEU* 4.9 1.8 - - + -
333B TRP* 4.1 9.2 - - + -
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Residues in contact with CYS 300 (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 TRP 3.2 5.1 + - - -
297A ARG 3.4 13.7 - - - +
298A GLU 3.1 0.6 - - - -
299A MSE 1.3 77.9 - - - +
301A HIS* 1.3 72.4 + - + +
303A ILE* 3.6 2.4 + - - +
304A MSE 3.3 42.8 + - - +
303B ILE* 6.0 0.2 - - - -
333B TRP* 3.5 64.8 - - + +
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Residues in contact with HIS 301 (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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273A ARG* 3.8 24.5 - - - +
297A ARG* 3.3 39.2 + - + +
298A GLU* 3.2 6.5 + - - -
300A CYS* 1.3 83.1 - - - +
302A ALA* 1.3 60.2 + - - +
304A MSE 4.7 7.4 - - + +
305A LEU* 2.9 46.9 + - + +
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Residues in contact with ALA 302 (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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273A ARG* 3.8 10.4 - - + +
292A ILE* 4.7 2.0 - - + -
293A ALA* 4.1 20.0 - - + -
298A GLU 3.2 13.0 + - - +
299A MSE 3.7 9.0 - - - +
301A HIS* 1.3 76.6 - - - +
303A ILE* 1.3 55.4 - - - +
306A GLN 3.0 6.9 + - - -
307A SER* 2.7 45.3 + - - -
308A VAL* 4.0 17.3 - - + -
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Residues in contact with ILE 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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299A MSE 3.2 39.1 + - + +
300A CYS 4.2 2.5 - - - +
302A ALA* 1.3 79.2 - - - +
304A MSE 1.3 61.6 + - - +
306A GLN* 3.3 17.2 + - - +
308A VAL* 4.2 14.4 - - + -
311A PRO* 5.6 0.2 - - + -
329A LEU* 4.2 12.8 - - + -
333A TRP* 4.1 19.1 - - + -
335A LEU* 4.0 29.4 - - + -
300B CYS* 6.0 1.1 - - - -
304B MSE 3.7 31.1 - - + +
333B TRP* 4.2 14.8 - - + -
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Residues in contact with MSE 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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300A CYS* 3.3 34.2 + - - +
301A HIS* 4.1 7.9 - - - +
302A ALA 3.2 0.2 - - - -
303A ILE* 1.3 76.7 - - - +
305A LEU* 1.3 61.2 + - + +
306A GLN* 2.9 15.2 + - - +
303B ILE* 3.8 17.3 - - - +
304B MSE 3.5 39.2 - - + +
306B GLN* 3.5 31.4 - - + +
333B TRP* 5.5 1.1 - - - -
304C MSE 5.1 7.9 - - + +
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Residues in contact with LEU 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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271A SER* 4.8 1.6 - - - +
273A ARG* 4.0 17.9 - - + -
274A GLU* 3.9 37.9 - - + +
277A ALA* 3.2 19.2 - - + +
281A ARG* 4.1 9.7 + - - +
301A HIS* 2.9 29.8 + - + +
304A MSE 1.3 74.1 - - + +
306A GLN* 1.3 68.2 + - - +
307A SER* 3.7 11.0 - - - +
306C GLN* 4.8 0.3 + - - -
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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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277A ALA* 4.0 6.7 - - + +
280A ARG* 3.4 38.4 + - - +
281A ARG* 5.5 0.2 - - - +
302A ALA 3.0 4.4 + - - -
303A ILE* 3.6 15.4 + - - +
304A MSE 2.9 11.2 + - - +
305A LEU* 1.3 82.9 - - - +
307A SER* 1.3 61.5 + - - +
308A VAL 3.4 6.4 - - - +
304B MSE 3.7 18.8 - - - +
280C ARG* 5.1 0.9 + - - -
281C ARG* 3.7 25.6 + - - +
304C MSE 4.3 4.0 + - - +
305C LEU 4.1 4.0 + - - -
306C GLN* 3.1 51.7 - - + +
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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