Contacts of the helix formed by residues 408 - 416 (chain A) in PDB entry 1W1J
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 TYR 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.9 23.8 - + - -
52A MET* 6.4 3.4 - - + -
104A ARG* 6.2 0.4 - - - -
149A HIS* 2.7 52.9 + + - +
171A LEU* 4.4 9.4 - - + -
172A GLY* 3.5 15.7 + - - -
173A GLY* 3.5 23.6 + - - -
407A THR* 1.3 81.4 - - - +
409A ASP* 1.3 69.7 + - - +
410A GLU 3.3 2.7 - - - -
411A LEU* 3.1 29.8 + - + +
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Residues in contact with ASP 409 (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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320A VAL* 4.4 10.7 - - + +
397A VAL* 3.6 35.0 - - + +
407A THR* 3.8 14.7 - - - +
408A TYR* 1.3 80.3 + - - +
410A GLU* 1.3 54.4 + - + +
411A LEU* 2.7 17.0 + - - +
412A LYS* 3.2 18.5 + - - +
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Residues in contact with GLU 410 (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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170A ASP* 4.1 31.5 + - + +
171A LEU* 4.1 5.6 - - + -
312A ARG* 2.5 38.7 + - - -
320A VAL* 4.2 15.2 - - + +
394A VAL* 4.7 2.9 - - + -
397A VAL* 4.0 19.3 - - + +
398A ARG* 2.5 38.4 + - - +
401A THR* 5.1 2.4 + - - -
408A TYR 3.3 1.2 - - - -
409A ASP* 1.3 71.4 - - + +
411A LEU* 1.3 60.0 + - - +
412A LYS 3.2 1.3 - - - -
413A TRP* 3.0 34.9 + - + +
1561A FAD 3.9 5.2 - - + +
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Residues in contact with LEU 411 (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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51A TYR* 3.7 39.0 - - + -
52A MET* 4.8 16.4 - - + -
171A LEU* 3.8 27.7 - - + +
408A TYR* 3.1 23.1 + - + +
409A ASP 2.7 5.6 + - - +
410A GLU* 1.3 74.3 - - - +
412A LYS* 1.3 66.4 + - - +
413A TRP 3.2 0.2 - - - -
414A ILE* 3.1 52.1 + - + +
415A ASP* 4.3 3.1 + - - +
1561A FAD 4.3 0.9 - - + -
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Residues in contact with LYS 412 (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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319A ALA 3.7 5.8 - - - +
320A VAL* 3.6 26.7 - - - +
321A LEU 5.7 0.4 - - - -
322A GLY* 5.6 7.2 - - - -
323A ASP 6.0 1.1 - - - +
409A ASP 3.2 11.0 + - - +
410A GLU 3.2 0.2 - - - -
411A LEU* 1.3 79.1 - - - +
413A TRP* 1.3 52.3 + - - +
415A ASP* 2.5 59.7 + - + +
416A TRP 4.0 0.2 + - - -
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Residues in contact with TRP 413 (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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170A ASP* 5.7 1.4 + - - +
312A ARG* 5.7 0.2 - - - +
316A LEU* 3.5 28.5 - - + +
319A ALA* 3.3 36.7 + - + +
320A VAL* 4.0 14.5 - - + +
410A GLU* 3.0 31.5 + - + +
411A LEU 3.2 1.6 - - - -
412A LYS* 1.3 77.3 - - - +
414A ILE* 1.3 63.5 + - - +
415A ASP 2.9 1.9 + - - -
416A TRP* 3.2 19.0 + - - +
422A HIS* 3.2 39.0 - + + -
424A PHE* 3.5 21.5 - + - -
455A ILE* 5.2 2.7 - - + -
470A CYS* 3.6 21.8 - - + -
472A VAL* 3.5 21.8 - - + +
1561A FAD 3.7 27.4 - + + +
1562A EUG 4.7 5.9 - - + +
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Residues in contact with ILE 414 (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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51A TYR* 6.1 0.4 - - + -
61A HIS* 3.8 21.8 - - + +
411A LEU* 3.2 39.9 - - + +
412A LYS 2.8 0.6 + - - -
413A TRP* 1.3 83.9 - - + +
415A ASP* 1.3 62.0 + - - +
416A TRP* 3.3 2.1 + - - -
420A GLY* 3.1 40.9 - - - +
421A ALA* 3.9 2.7 + - - -
422A HIS* 3.6 18.8 - - + +
472A VAL* 4.6 6.3 - - - +
1561A FAD 3.6 28.7 - - + -
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Residues in contact with ASP 415 (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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319A ALA 6.0 0.2 - - - -
323A ASP* 3.2 21.1 - - + +
411A LEU 4.9 4.2 - - - +
412A LYS* 2.5 44.7 + - + +
414A ILE* 1.3 83.6 - - - +
416A TRP* 1.3 63.6 + - - +
417A LEU* 3.1 9.2 + - - +
418A PRO* 4.8 4.0 - - - +
420A GLY 4.0 17.2 + - - +
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Residues in contact with TRP 416 (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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315A LEU* 4.0 29.4 - - + -
318A ALA* 4.2 1.1 - - + -
319A ALA* 3.4 36.5 + - + +
322A GLY 3.7 13.7 - - - -
323A ASP* 3.7 11.4 - - - +
324A LYS* 3.1 67.4 + - + +
325A ARG 4.8 0.2 + - - -
327A TYR* 4.0 15.9 - + - -
334A LEU* 4.0 18.6 - - + -
412A LYS 4.0 0.2 + - - -
413A TRP* 3.2 16.2 + - - +
414A ILE 3.3 1.2 - - - -
415A ASP* 1.3 77.9 - - - +
417A LEU* 1.3 75.8 + - + +
418A PRO* 4.5 1.7 - - - +
453A ASP* 3.3 24.6 + - + +
455A ILE* 4.4 12.6 - - + -
472A VAL* 3.7 14.4 - - + -
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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