Contacts of the helix formed by residues 326 - 338 (chain A) in PDB entry 3N1Z
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 GLU 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLN 4.9 4.7 - - - +
323A ASP* 3.1 6.3 + - - +
324A LEU 3.4 0.2 - - - -
325A ASP* 1.3 107.7 - - + +
327A THR* 1.3 66.9 + - - +
328A HIS* 3.4 2.7 - - - -
329A HIS* 2.9 26.6 + - - +
330A GLY 3.4 3.3 + - - -
368A THR* 4.8 1.0 + - - -
369A TRP* 2.9 28.6 + - + +
406A HIS* 3.4 28.3 - - + +
407A THR* 2.4 34.6 + - - +
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Residues in contact with THR 327 (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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266A TRP* 3.8 14.4 + - + +
267A LYS* 4.7 9.4 - - - -
270A SER* 3.4 26.5 - - - +
323A ASP* 3.2 31.2 + - - +
326A GLU* 1.3 75.9 - - - +
328A HIS* 1.3 64.2 + - - +
330A GLY* 3.2 4.7 + - - +
331A MET* 3.0 35.3 + - + +
369A TRP* 5.5 0.7 - - - -
405A ALA 5.4 6.1 - - - +
406A HIS* 4.3 11.0 + - - -
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TRP* 5.3 0.6 - - - -
270A SER* 3.3 23.3 - - - +
274A GLY* 3.8 31.0 - - - -
275A PRO* 3.7 4.4 - - + +
278A ASP* 2.8 29.2 + - + -
279A TYR* 4.5 3.4 - + - -
290A PHE* 3.2 29.7 - + + +
323A ASP 5.3 0.2 + - - -
324A LEU* 3.6 20.1 + - - -
326A GLU 3.1 2.2 + - - -
327A THR* 1.3 78.2 - - - +
329A HIS* 1.3 82.6 + + - +
331A MET 3.7 0.2 - - - -
332A HIS* 2.9 30.3 + - - +
362A TYR* 3.3 16.6 - - - -
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Residues in contact with HIS 329 (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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278A ASP* 4.0 1.8 - - - -
279A TYR* 2.5 38.3 + + - +
325A ASP 3.0 29.9 + - - -
326A GLU 2.9 12.6 + - - +
328A HIS* 1.3 95.5 + + - +
330A GLY* 1.3 58.2 + - - +
332A HIS* 3.2 5.9 + - - +
333A LEU* 2.8 30.3 + - - +
358A LEU* 4.5 1.8 - - + -
362A TYR* 3.5 36.7 - + - -
365A TRP* 3.2 18.4 + + - -
369A TRP* 3.5 30.3 - + + -
373A TRP* 5.6 0.5 + - - -
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU 3.4 0.4 + - - -
327A THR* 3.2 7.1 + - - -
329A HIS* 1.3 78.3 - - - +
331A MET* 1.3 54.6 + - - +
333A LEU 3.2 0.2 + - - -
334A GLY* 2.7 32.6 + - - -
369A TRP* 3.2 29.9 - - - -
403A PRO* 5.7 0.7 - - - +
405A ALA* 4.4 11.1 - - - +
14C PHE* 3.3 14.0 - - - -
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Residues in contact with MET 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 4.1 19.7 - - - +
270A SER* 3.2 35.4 - - - +
271A VAL* 3.9 22.9 - - + -
275A PRO* 4.3 2.0 - - + -
327A THR* 3.0 25.7 + - + +
328A HIS 3.4 1.1 + - - +
330A GLY* 1.3 75.5 - - - +
332A HIS* 1.3 56.9 + - - +
334A GLY* 3.9 0.8 - - - -
335A VAL* 3.0 35.2 + - - +
400A CYS* 5.3 0.2 - - - -
402A LEU* 3.9 30.5 - - + -
403A PRO* 3.8 34.3 - - - +
405A ALA* 5.7 6.5 - - + +
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Residues in contact with HIS 332 (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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275A PRO* 3.7 17.8 - - + +
279A TYR* 3.3 45.2 - + + -
280A TYR* 3.7 22.1 + + - -
328A HIS 2.9 18.8 + - - +
329A HIS 3.5 4.0 - - - +
331A MET* 1.3 75.8 - - - +
333A LEU* 1.3 60.8 + - - +
335A VAL* 3.8 2.5 - - - +
336A TRP* 2.9 33.9 + - + +
346A PRO* 5.5 0.2 - - + -
347A ALA 3.0 25.1 - - - -
348A ALA* 2.8 22.6 + - - -
373A TRP* 4.0 14.8 - + - -
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Residues in contact with LEU 333 (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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329A HIS 2.8 16.5 + - - +
330A GLY* 3.8 3.6 - - - +
332A HIS* 1.3 76.6 - - - +
334A GLY* 1.3 57.6 + - - +
337A TYR* 2.8 37.2 + - + +
369A TRP* 4.1 12.1 - - + +
372A CYS* 3.7 25.4 - - + -
373A TRP* 3.5 43.3 - - + +
376A ILE* 3.7 23.8 - - + -
14C PHE* 3.6 38.1 - - + -
42C ARG* 4.8 1.6 - - - -
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Residues in contact with GLY 334 (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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330A GLY 2.7 16.2 + - - -
331A MET* 3.9 1.8 - - - -
333A LEU* 1.3 77.4 - - - +
335A VAL* 1.3 50.0 + - - +
338A TRP* 2.8 47.9 + - - +
403A PRO* 5.2 11.0 - - - -
502A P6G 5.1 4.7 - - - -
14C PHE* 3.4 18.7 - - - -
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Residues in contact with VAL 335 (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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167A TRP* 3.5 37.0 - - + -
271A VAL* 4.1 14.4 - - + +
275A PRO* 6.0 2.2 - - + -
280A TYR* 4.1 8.7 - - - +
331A MET 3.0 21.4 + - - +
332A HIS* 3.9 5.4 - - - +
334A GLY* 1.3 74.2 - - - +
336A TRP* 1.3 58.1 + - - +
338A TRP* 3.3 5.0 - - - -
339A ARG* 3.0 26.3 + - - +
342A VAL* 4.3 7.1 - - + +
344A TRP* 3.9 27.4 - - + -
346A PRO* 3.9 15.5 - - + +
403A PRO* 5.9 1.1 - - + +
502A P6G 5.2 0.2 - - - +
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Residues in contact with TRP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A HIS* 2.9 22.5 + - + +
333A LEU* 3.9 2.2 - - + +
335A VAL* 1.3 74.4 - - - +
337A TYR* 1.3 73.1 + - + +
339A ARG* 2.9 67.2 + - - +
346A PRO* 3.6 35.6 + - + -
347A ALA 4.2 0.4 - - - -
348A ALA* 3.7 15.8 - - + +
373A TRP* 3.4 27.6 - + + -
376A ILE* 3.4 43.1 - - + -
380A LEU* 4.3 6.5 - - + -
388A THR* 4.2 10.3 - - - -
481A ASP* 2.8 29.9 + - - +
485A TYR* 4.1 10.8 - + - -
487A TRP* 4.3 7.2 - + - -
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Residues in contact with TYR 337 (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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333A LEU* 2.8 23.8 + - + +
334A GLY 3.7 2.9 - - - +
336A TRP* 1.3 82.6 - + + +
338A TRP* 1.3 74.4 + + + +
339A ARG* 3.2 6.4 + - - +
340A PRO* 4.4 0.5 - - - +
376A ILE* 4.1 19.7 - - + -
387A LEU 2.9 20.8 + - - -
388A THR* 3.2 33.2 - - - +
389A VAL* 3.1 11.4 + - - -
390A PRO* 3.4 39.4 - - + +
14C PHE* 5.1 0.7 - - + -
41C ARG* 3.3 26.5 + - - -
42C ARG* 3.3 42.8 - - - +
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Residues in contact with TRP 338 (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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167A TRP* 6.0 0.2 - - + -
334A GLY* 2.8 35.6 + - - +
335A VAL* 3.3 6.4 - - - +
337A TYR* 1.3 90.9 - + + +
339A ARG* 1.3 62.9 + - - +
340A PRO* 3.3 5.6 - - - -
341A THR* 2.6 48.0 + - + +
342A VAL* 4.2 0.5 + - - +
390A PRO* 3.0 37.1 - - + +
392A THR 3.1 23.8 + - - -
393A LEU* 4.4 0.6 - - - +
394A PRO* 3.9 29.1 - - + +
403A PRO* 6.4 0.9 - - + -
502A P6G 4.1 34.2 + - - +
14C PHE* 4.4 7.0 - + - -
15C VAL* 4.2 16.8 - - + -
17C GLN* 3.5 28.3 - - - -
42C ARG* 3.8 11.7 - - - -
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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