Contacts of the helix formed by residues 356 - 367 (chain B) in PDB entry 3W8I
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 ILE 356 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 4.2 32.1 - - + +
69A LYS* 4.0 41.8 - - + +
70A LYS* 4.2 20.4 - - + -
352B CYS* 2.8 40.9 + - + +
354B SER 3.5 0.2 - - - -
355B MET* 1.3 94.4 - - + +
357B ILE* 1.3 68.1 + - + +
359B PRO* 3.3 4.8 - - - +
360B ALA* 3.1 27.8 + - + +
400B VAL* 4.9 2.5 - - + -
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Residues in contact with ILE 357 (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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66A ILE* 4.0 27.1 - - + -
352B CYS 2.8 19.7 + - - +
353B LEU* 3.4 21.1 - - + +
356B ILE* 1.3 72.7 - - - +
358B THR* 1.3 59.6 + - - +
360B ALA* 4.4 1.8 - - - -
361B PHE* 2.9 59.9 + - + +
382B GLU* 4.6 7.0 - - + -
385B ILE* 4.0 17.5 - - + -
396B THR* 3.7 25.1 - - + -
399B MET* 4.4 13.2 - - + -
400B VAL* 4.5 7.4 - - + -
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Residues in contact with THR 358 (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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353B LEU* 3.0 21.3 + - - +
354B SER* 4.4 7.0 - - - -
357B ILE* 1.3 75.9 - - - +
359B PRO* 1.4 69.5 - - + +
361B PHE* 3.8 1.9 - - - +
362B ALA* 3.0 24.2 + - + +
382B GLU* 2.8 29.7 + - - +
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Residues in contact with PRO 359 (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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69A LYS* 4.5 16.6 - - - -
354B SER 3.7 13.2 - - - +
355B MET 3.8 15.0 - - - +
356B ILE 3.3 16.2 - - - +
358B THR* 1.4 96.1 - - + +
360B ALA* 1.3 61.0 + - - +
362B ALA* 3.1 8.5 + - + +
363B GLU* 2.9 32.0 + - + +
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Residues in contact with ALA 360 (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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65A LYS* 3.5 31.5 - - + +
66A ILE* 4.7 13.5 - - + -
69A LYS* 5.0 5.3 - - + +
356B ILE* 3.1 21.4 + - + +
357B ILE* 3.6 4.5 - - - +
359B PRO* 1.3 77.8 - - - +
361B PHE* 1.3 65.0 + - + +
363B GLU* 3.3 7.0 + - - +
364B LEU* 2.9 31.2 + - + +
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Residues in contact with PHE 361 (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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62A ILE* 4.1 29.8 - - + -
66A ILE* 5.2 1.1 - - + -
357B ILE* 2.9 38.1 + - + +
358B THR 3.8 2.9 - - - +
360B ALA* 1.3 79.7 - - + +
362B ALA* 1.3 66.9 + - - +
364B LEU* 3.2 13.3 + - + +
365B LYS* 2.9 30.5 + - - +
378B ILE* 3.4 42.4 - - + +
381B LEU* 3.8 31.0 - - + -
382B GLU* 3.9 28.0 - - + +
385B ILE* 3.9 15.0 - - + -
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Residues in contact with ALA 362 (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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358B THR* 3.0 16.7 + - + +
359B PRO* 3.3 12.1 - - + +
361B PHE* 1.3 76.1 - - - +
363B GLU* 1.3 57.5 + - + +
365B LYS* 3.2 16.2 + - - +
366B GLN* 2.9 33.1 + - - +
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Residues in contact with GLU 363 (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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65A LYS* 2.7 43.5 + - - +
68A GLU* 4.1 2.8 - - - +
69A LYS* 2.4 39.1 + - - -
359B PRO* 2.9 19.6 + - - +
360B ALA 3.5 6.1 - - - +
361B PHE 3.3 0.2 - - - -
362B ALA* 1.3 72.6 - - + +
364B LEU* 1.3 62.3 + - - +
366B GLN* 2.8 37.3 + - - +
367B GLN* 2.9 17.3 + - - +
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Residues in contact with LEU 364 (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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58A LEU* 4.8 6.1 - - + -
61A ASP* 3.7 27.6 - - + +
62A ILE* 3.6 36.6 - - + +
65A LYS* 3.9 11.0 - - + -
360B ALA 2.9 19.4 + - - +
361B PHE* 3.2 24.0 + - + +
363B GLU* 1.3 75.5 - - - +
365B LYS* 1.3 58.5 + - - +
367B GLN* 3.3 36.6 + - - +
374B ARG* 2.6 29.7 + - - +
378B ILE* 4.0 12.8 - - + -
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Residues in contact with LYS 365 (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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361B PHE* 2.9 20.7 + - - +
362B ALA* 3.4 13.7 - - - +
364B LEU* 1.3 74.5 - - - +
366B GLN* 1.3 63.4 + - + +
367B GLN 3.1 1.6 - - - -
368B ASP 3.0 15.4 + - - +
369B GLU* 3.1 17.1 + - - -
375B ASN* 3.6 39.2 - - + +
378B ILE* 3.9 23.8 - - + +
379B GLU* 3.2 41.7 + - - +
382B GLU* 5.0 8.1 + - - -
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Residues in contact with GLN 366 (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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362B ALA* 2.9 18.4 + - - +
363B GLU* 2.8 31.3 + - - +
365B LYS* 1.3 76.0 - - + +
367B GLN* 1.3 60.2 + - - +
368B ASP 3.1 1.0 + - - -
369B GLU* 4.2 18.1 + - + +
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Residues in contact with GLN 367 (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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61A ASP* 3.9 9.7 + - - +
65A LYS* 4.0 17.4 - - - +
363B GLU* 2.9 15.8 + - + +
364B LEU* 3.3 32.4 - - - +
365B LYS 3.1 0.6 - - - -
366B GLN* 1.3 78.4 - - - +
368B ASP* 1.3 60.4 + - + +
374B ARG* 3.2 25.0 + - - +
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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