Contacts of the helix formed by residues 316 - 328 (chain B) in PDB entry 3EZB
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 THR 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 4.2 21.3 - - + +
75A GLY* 5.9 1.8 - - - -
76A HIS* 3.8 28.9 - - + +
126A ARG* 3.5 30.5 - - + +
129A ASP* 3.8 14.4 + - + +
315B HIS* 1.3 82.9 + - - +
317B ARG* 1.3 65.9 + - - +
319B ALA* 3.5 3.4 - - + +
320B ALA* 3.1 20.9 + - + +
347B LEU* 5.7 7.4 - - + -
351B GLN* 5.7 0.7 - - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU* 4.4 16.6 + - - +
68A GLU* 2.4 57.8 + - - +
71A ALA* 3.1 33.0 - - - +
72A ILE* 3.8 17.9 - - + +
315B HIS* 3.5 18.0 + - + -
316B THR* 1.3 83.6 - - - +
318B PRO* 1.3 75.6 - - + +
320B ALA* 3.1 13.0 + - - +
321B GLN* 2.6 46.0 + - - +
384B LEU* 5.0 1.2 - - - +
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Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLY 4.2 2.9 - - - +
314B LEU* 3.6 24.2 - - + -
315B HIS* 3.1 44.0 - - + +
317B ARG* 1.3 103.1 - - + +
319B ALA* 1.3 54.9 + - - +
321B GLN* 3.1 15.8 + - - +
322B PHE* 2.7 29.3 + - - +
384B LEU* 4.0 20.4 - - + +
385B GLU* 4.7 11.0 - - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 2.9 34.1 - - - +
314B LEU* 4.3 10.2 - - + +
315B HIS 3.1 11.1 + - - +
316B THR* 3.5 5.8 - - + +
317B ARG 3.1 0.4 - - - -
318B PRO* 1.3 77.2 - - - +
320B ALA* 1.3 65.6 + - - +
322B PHE* 2.8 9.8 + - - +
323B VAL* 2.8 30.1 + - + +
347B LEU* 4.5 11.9 - - + -
350B LEU* 5.9 2.0 - - + -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.4 21.1 - - + +
72A ILE* 4.9 0.9 - - - -
74A GLU* 4.6 2.4 - - + +
75A GLY* 3.3 34.5 - - - +
78A MET* 3.5 6.5 - - + +
316B THR 3.1 8.7 + - - +
317B ARG 3.1 10.3 + - - +
319B ALA* 1.3 78.0 - - - +
321B GLN* 1.3 58.6 + - - +
323B VAL* 5.0 0.9 - - - -
324B LYS* 2.9 33.2 + - - +
347B LEU* 6.1 2.6 - - - +
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Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 5.1 5.9 + - - -
71A ALA* 4.6 8.1 - - + -
317B ARG* 2.6 49.7 + - - +
318B PRO* 3.1 10.5 + - - +
319B ALA 3.1 0.6 - - - -
320B ALA* 1.3 78.4 - - - +
322B PHE* 1.3 64.5 + - - +
324B LYS* 3.7 19.4 - - - +
325B GLU* 3.0 25.6 + - - +
380B LEU* 3.7 17.4 - - + +
384B LEU* 3.1 30.7 - - + +
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B LEU* 4.8 11.7 - - + -
318B PRO 2.7 17.9 + - - +
319B ALA* 2.8 13.6 + - - +
321B GLN* 1.3 75.6 - - - +
323B VAL* 1.3 72.8 + - + +
325B GLU* 3.5 2.8 + - - +
326B ALA* 3.2 19.5 + - + +
333B ILE* 5.9 0.4 - - + -
335B VAL* 4.0 22.0 - - + -
344B ALA* 3.8 24.2 - - + -
350B LEU* 4.7 8.5 - - + -
355B LEU* 6.5 0.7 - - + -
363B ILE* 4.4 18.4 - - + -
377B LEU* 4.4 18.8 - - + +
380B LEU* 4.5 8.5 - - + +
381B MET* 3.3 46.0 - - + -
384B LEU* 4.9 8.7 - - + -
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET* 3.9 12.3 - - + -
319B ALA* 2.8 20.8 + - - +
320B ALA* 5.0 0.4 - - - -
322B PHE* 1.3 74.3 - - + +
324B LYS* 1.3 65.9 + - - +
326B ALA* 4.3 1.1 - - - -
327B LYS* 2.9 52.0 + - + +
344B ALA 3.2 20.2 - - - +
345B LYS* 4.7 1.3 - - - -
346B SER 4.8 0.2 - - - +
347B LEU* 4.6 18.8 - - + +
350B LEU* 3.1 36.3 - - + -
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 5.7 3.4 - - - +
74A GLU* 2.9 44.3 + - + +
78A MET* 3.4 21.0 - - + +
320B ALA 2.9 19.3 + - - +
321B GLN* 3.7 23.5 - - - +
322B PHE 3.2 0.2 - - - -
323B VAL* 1.3 80.0 - - - +
325B GLU* 1.3 64.8 + - - +
327B LYS* 3.6 2.6 + - - +
328B GLY* 3.5 13.5 + - - -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B GLN 3.0 17.6 + - - +
322B PHE 4.0 0.7 - - - +
324B LYS* 1.3 79.8 - - - +
326B ALA* 1.3 63.3 + - - +
328B GLY* 3.1 13.0 + - - -
329B PHE* 3.5 25.9 - - + -
376B HIS* 4.9 15.3 - - + +
377B LEU* 3.8 19.3 - - + -
380B LEU* 3.7 21.4 - - + +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PHE* 3.2 16.1 + - + +
323B VAL* 3.7 3.8 - - - +
325B GLU* 1.3 74.2 - - - +
327B LYS* 1.3 53.4 + - - +
328B GLY 2.6 16.8 + - - -
329B PHE* 2.7 26.9 + - - +
333B ILE* 3.8 20.4 - - + +
344B ALA* 3.9 30.3 - - + +
345B LYS* 5.4 0.7 - - - +
377B LEU* 4.1 12.5 - - + +
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Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET* 3.7 30.7 - - + -
79A LEU* 6.1 1.3 - - - +
82A ASP* 4.4 19.3 + - - +
323B VAL* 2.9 45.2 + - + +
324B LYS 4.1 4.9 - - - +
326B ALA* 1.3 71.4 - - - +
328B GLY* 1.3 60.5 + - - +
329B PHE 3.2 8.2 + - - +
345B LYS* 3.0 42.5 + - + +
346B SER* 5.3 0.9 - - - +
347B LEU 5.6 0.9 - - - +
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LYS 3.5 6.3 + - - -
325B GLU* 3.1 11.5 + - - -
326B ALA 2.6 8.5 + - - -
327B LYS* 1.3 76.6 - - - +
329B PHE* 1.3 64.6 + - - -
330B THR* 4.1 2.1 + - - -
369B ASP* 5.3 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