Contacts of the helix formed by residues 433 - 445 (chain A) in PDB entry 2WWA
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 VAL 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.5 10.8 - - + +
288A LEU* 4.2 15.0 - - + -
429A THR* 3.2 18.2 + - - +
430A GLY* 4.2 6.1 - - - -
432A SER* 1.4 74.6 - - - +
434A LEU* 1.4 62.0 + - - +
435A SER 3.4 0.4 - - - -
436A LEU* 3.7 20.1 - - + +
437A ILE* 3.1 26.8 + - + +
35B PHE* 4.0 18.6 - - + -
36B LEU* 4.0 34.1 - - + -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 5.0 2.7 - - + -
263A LEU* 4.3 4.5 - - + -
288A LEU* 5.5 1.1 - - + -
289A LEU* 3.4 57.0 - - + +
292A GLY* 3.4 31.9 - - - +
293A CYS* 4.0 1.1 - - - +
296A VAL* 3.6 21.7 - - + +
430A GLY 3.6 14.4 - - - +
431A ALA* 4.1 5.2 - - - +
432A SER 3.4 0.2 - - - -
433A VAL* 1.4 80.3 - - - +
435A SER* 1.4 60.3 + - - +
436A LEU 3.2 0.4 - - - -
437A ILE* 3.5 11.1 + - + +
438A THR* 3.3 25.9 + - - +
454A VAL* 6.1 2.7 - - + -
455A VAL* 6.3 1.3 - - + -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 4.1 13.6 - - - +
299A SER* 4.8 2.0 - - - -
374A ILE* 3.3 55.2 + - - +
375A LEU* 3.6 7.6 - - - +
378A GLY* 4.7 2.0 - - - -
431A ALA 3.2 19.5 + - - -
432A SER* 3.4 13.3 + - - -
434A LEU* 1.4 77.2 - - - +
436A LEU* 1.4 58.7 + - - +
438A THR* 3.6 13.4 - - - +
439A VAL* 3.5 4.2 - - - +
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 5.1 9.9 - - - +
375A LEU* 4.0 23.3 - - + -
432A SER 3.5 16.7 + - - +
433A VAL* 3.7 21.1 - - + +
434A LEU 3.2 0.6 - - - -
435A SER* 1.4 82.0 + - - +
437A ILE* 1.4 58.2 + - - +
438A THR 3.4 0.2 - - - -
439A VAL* 3.2 25.6 - - + +
440A ILE* 3.3 19.9 + - + +
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Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE* 5.1 2.1 - - - +
259A ILE* 3.2 47.6 - - + +
260A VAL* 4.0 20.6 - - + +
263A LEU* 3.5 38.1 - - + -
433A VAL* 3.1 12.7 + - + +
434A LEU* 3.5 14.1 + - + +
436A LEU* 1.4 74.9 - - + +
438A THR* 1.4 67.8 + - - +
440A ILE* 3.6 12.5 - - + +
441A GLY* 3.3 17.8 + - - -
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Residues in contact with THR 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 5.8 0.2 - - - -
296A VAL* 4.6 11.0 - - + -
300A TYR* 5.5 9.4 - - + -
374A ILE* 5.1 3.8 - - + -
434A LEU* 3.3 20.2 + - - +
435A SER* 3.6 16.6 - - - +
437A ILE* 1.4 80.4 - - - +
439A VAL* 1.4 63.7 + - + +
441A GLY* 3.5 2.3 + - - -
442A GLU* 3.2 31.9 + - - +
451A ALA* 3.5 27.1 - - + +
454A VAL* 3.7 24.3 - - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PRO* 5.6 1.3 - - + -
367A PHE* 5.2 7.4 - - + -
370A TYR* 3.4 36.1 - - + -
371A SER* 4.3 18.8 - - - +
374A ILE* 3.8 19.3 - - + -
435A SER 3.5 12.6 - - - +
436A LEU* 3.2 25.6 - - + +
438A THR* 1.4 81.9 - - - +
440A ILE* 1.4 57.0 + - + +
442A GLU* 3.3 12.4 + - + +
443A SER* 2.9 33.3 + - - +
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Residues in contact with ILE 440 (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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259A ILE* 4.8 4.9 - - + -
367A PHE* 5.6 4.7 - - + -
436A LEU* 3.3 22.6 + - + +
437A ILE* 3.6 25.8 - - + +
438A THR 3.4 0.2 - - - -
439A VAL* 1.4 75.0 - - + +
441A GLY* 1.4 64.4 + - - +
443A SER* 3.6 22.4 - - - +
444A LEU* 3.7 15.3 - - + +
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Residues in contact with GLY 441 (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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256A ILE* 3.3 48.2 - - - +
259A ILE* 4.8 4.5 - - - -
437A ILE 3.3 10.9 + - - -
438A THR 4.0 2.5 - - - -
439A VAL 3.3 0.4 - - - -
440A ILE* 1.4 74.9 - - - +
442A GLU* 1.4 62.5 + - - +
443A SER 3.3 0.6 + - - -
444A LEU* 3.5 17.8 + - - +
445A GLY 3.4 4.7 - - - +
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Residues in contact with GLU 442 (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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256A ILE* 4.9 0.9 - - - -
300A TYR* 3.1 28.9 + - - -
352A PRO* 4.1 4.5 - - + +
353A PRO* 6.2 1.3 - - + -
354A THR* 3.0 37.9 + - + -
370A TYR* 3.6 19.0 + - + -
438A THR* 3.2 23.9 + - - +
439A VAL* 3.3 16.6 + - + +
441A GLY* 1.4 74.1 - - - +
443A SER* 1.4 57.7 + - - +
445A GLY 3.0 15.8 + - - -
447A LYS* 3.3 15.8 + - - -
450A ALA* 3.6 27.2 - - + +
451A ALA* 4.2 7.9 - - + -
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A PRO* 5.9 4.3 - - - -
354A THR* 5.3 1.1 - - - -
359A GLY* 3.4 23.3 + - - -
367A PHE* 3.3 37.9 - - - -
439A VAL* 2.9 19.7 + - - +
440A ILE* 3.6 18.1 - - - -
441A GLY 3.3 0.2 - - - -
442A GLU* 1.4 76.4 - - - +
444A LEU* 1.4 63.3 + - - +
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Residues in contact with LEU 444 (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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248A THR* 5.8 0.2 + - - -
252A ILE* 3.9 23.5 - - + +
255A ALA* 3.7 35.0 - - + +
256A ILE* 4.6 1.3 - - + +
259A ILE* 5.8 3.1 - - + -
357A PHE 4.6 0.2 - - - +
358A LYS* 4.1 7.8 - - - +
359A GLY 3.8 9.2 + - - -
440A ILE* 3.7 16.6 - - + +
441A GLY* 3.6 17.0 - - - +
442A GLU 3.3 0.4 - - - -
443A SER* 1.4 78.1 - - - +
445A GLY* 1.4 56.9 + - - +
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Residues in contact with GLY 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 3.8 7.5 - - - +
256A ILE* 4.0 2.1 - - - +
354A THR* 3.3 17.7 - - - -
355A SER 4.2 0.7 - - - -
357A PHE 3.9 13.2 - - - -
359A GLY 4.5 4.5 - - - -
441A GLY 3.4 10.9 - - - +
442A GLU* 3.0 12.5 + - - +
443A SER 4.4 1.1 - - - -
444A LEU* 1.4 78.4 - - - +
446A LEU* 1.4 67.3 + - - +
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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