Contacts of the helix formed by residues 433 - 444 (chain A) in PDB entry 3WOO
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 ASP 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ARG* 3.3 22.8 + - - +
428A GLY* 2.9 50.7 + - - +
430A GLN* 2.9 29.1 + - - +
432A ARG* 1.3 82.7 + - - +
434A LEU* 1.3 67.1 + - - +
435A PRO* 3.4 3.6 - - - -
436A ALA* 3.1 12.3 + - + +
437A ILE* 3.0 24.4 + - + +
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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
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414A LEU* 3.9 31.4 - - + -
418A ARG* 4.0 24.7 - - - +
425A ARG* 5.7 2.7 - - - +
429A TYR 4.8 0.4 - - - +
430A GLN 3.4 14.0 + - - +
431A GLU* 3.1 34.0 + - + +
433A ASP* 1.3 78.7 - - - +
435A PRO* 1.3 67.0 - - + +
437A ILE* 3.8 7.2 - - + +
438A GLU* 3.0 26.4 + - - +
510A PHE* 3.9 16.4 - - + -
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Residues in contact with PRO 435 (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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120A PRO* 5.8 0.2 - - - +
121A ASN* 3.7 5.2 - - - +
123A ARG* 4.2 17.7 - - - +
194A LYS* 4.5 17.3 - - - +
431A GLU 3.7 8.1 - - - +
432A ARG* 3.8 11.0 - - - +
433A ASP 3.4 4.9 - - - -
434A LEU* 1.3 94.1 - - + +
436A ALA* 1.3 56.2 + - - +
438A GLU* 3.5 5.8 + - + +
439A GLY* 2.9 23.7 + - - -
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Residues in contact with ALA 436 (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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121A ASN* 2.9 36.3 + - - +
123A ARG* 4.9 5.6 - - - +
432A ARG 5.5 0.4 + - - +
433A ASP* 3.1 14.3 + - + +
435A PRO* 1.3 76.1 - - - +
437A ILE* 1.3 68.0 + - + +
440A GLY* 3.0 9.4 + - - -
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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
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410A GLN* 3.9 36.9 - - + +
411A LEU* 5.2 2.9 - - + -
414A LEU* 4.5 9.4 - - + -
428A GLY 3.3 27.4 - - - +
429A TYR* 4.4 18.2 - - + -
433A ASP* 3.0 24.1 + - + +
434A LEU* 3.8 15.5 - - + +
436A ALA* 1.3 80.2 - - + +
438A GLU* 1.3 63.4 + - - +
440A GLY* 3.2 1.4 + - - -
441A LEU* 3.1 25.7 + - + +
510A PHE* 3.6 23.6 - - + -
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Residues in contact with GLU 438 (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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434A LEU 3.0 17.2 + - - +
435A PRO* 3.8 5.9 - - + +
437A ILE* 1.3 78.0 - - - +
439A GLY* 1.3 60.7 + - - +
441A LEU* 3.2 17.3 + - - +
442A LYS* 3.3 35.1 + - + +
507A LEU* 3.5 26.8 - - + +
510A PHE* 3.7 32.7 - - + -
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Residues in contact with GLY 439 (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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120A PRO* 3.7 18.9 - - - +
121A ASN* 3.3 20.9 - - - -
435A PRO 2.9 13.3 + - - -
437A ILE 3.3 0.4 - - - -
438A GLU* 1.3 77.0 - - - +
440A GLY* 1.3 57.0 + - - +
442A LYS* 3.3 6.0 + - - +
443A GLN* 2.9 33.4 + - - +
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Residues in contact with GLY 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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121A ASN* 3.4 9.1 - - - +
436A ALA 3.0 16.4 + - - -
437A ILE 3.7 1.8 - - - -
439A GLY* 1.3 77.3 - - - +
441A LEU* 1.4 62.3 + - - +
443A GLN* 3.3 8.5 + - - +
444A LEU* 3.1 23.9 + - - +
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Residues in contact with LEU 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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407A SER* 4.1 21.5 - - - +
410A GLN* 4.2 15.5 - - - +
411A LEU* 3.7 33.9 - - + -
437A ILE* 3.1 17.5 + - + +
438A GLU* 3.2 9.1 + - - +
440A GLY* 1.4 77.8 - - - +
442A LYS* 1.3 57.6 + - - +
444A LEU* 3.9 2.9 + - + +
503A THR* 4.1 3.5 - - - +
506A ARG* 2.9 54.9 + - + +
507A LEU* 3.9 13.5 - - + -
510A PHE* 3.9 24.5 - - + -
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Residues in contact with LYS 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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120A PRO* 4.7 13.0 - - + -
438A GLU* 3.3 31.0 + - + +
439A GLY* 3.3 10.2 + - - +
440A GLY 3.2 0.2 - - - -
441A LEU* 1.3 75.0 - - - +
443A GLN* 1.3 65.9 + - - +
444A LEU 3.1 1.6 - - - -
445A GLU* 3.1 23.7 + - - +
446A ARG* 4.5 1.0 + - - +
503A THR* 4.0 13.7 - - + -
507A LEU* 3.4 35.3 - - + +
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Residues in contact with GLN 443 (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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94A LEU* 3.7 44.6 - - + +
118A ALA 4.8 0.6 + - - -
119A GLY* 3.7 2.6 - - - -
120A PRO* 3.4 18.5 - - + +
121A ASN* 3.0 45.8 + - - +
122A ALA 4.5 0.2 - - - +
439A GLY 2.9 19.8 + - - +
440A GLY* 3.3 7.4 + - - +
442A LYS* 1.3 76.7 - - - +
444A LEU* 1.3 62.7 + - - +
446A ARG* 3.1 14.6 + - - +
447A ARG* 3.8 23.4 + - - +
805A GOL 5.2 6.5 + - - -
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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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403A ALA* 4.0 22.7 - - + +
404A MET* 4.1 14.1 - - + -
407A SER* 3.7 23.6 - - - +
440A GLY 3.1 16.0 + - - +
441A LEU* 3.9 7.6 - - - +
442A LYS 3.1 1.0 - - - -
443A GLN* 1.3 74.3 - - - +
445A GLU* 1.3 61.2 + - - +
446A ARG 3.1 0.2 - - - -
447A ARG* 2.8 35.1 + - + +
448A TYR* 3.2 22.5 + - + +
506A ARG* 3.8 20.4 - - - +
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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