Contacts of the helix formed by residues 433 - 444 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 3.3 23.7 + - - +
427B SER* 4.5 0.3 - - - -
428B GLY* 2.9 50.7 + - - +
429B TYR* 4.4 0.9 - - - -
430B GLN* 2.9 30.2 + - - +
432B ARG* 1.3 86.3 + - - +
434B LEU* 1.3 65.0 + - - +
435B PRO* 3.4 2.7 - - - -
436B ALA* 3.3 9.3 + - + +
437B ILE* 3.1 24.3 + - + +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 3.8 30.3 - - + -
418B ARG* 4.2 17.7 - - - +
425B ARG* 5.8 1.8 - - - +
429B TYR 5.0 0.2 - - - +
430B GLN 3.5 9.7 + - - +
431B GLU* 3.1 37.8 + - + +
433B ASP* 1.3 78.4 - - - +
435B PRO* 1.3 68.1 - - + +
437B ILE* 3.3 6.7 + - + +
438B GLU* 2.9 26.8 + - - +
510B PHE* 3.8 24.7 - - + -
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Residues in contact with PRO 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 5.6 0.5 - - - +
121B ASN* 3.8 2.2 - - - +
123B ARG* 4.1 18.6 - - - +
194B LYS* 5.0 14.8 - - + +
431B GLU 3.8 7.4 - - - +
432B ARG* 3.9 9.6 - - - +
433B ASP 3.5 3.8 - - - -
434B LEU* 1.3 94.4 - - + +
436B ALA* 1.3 56.8 + - - +
438B GLU* 3.8 6.1 - - + +
439B GLY* 2.9 26.7 + - - -
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 2.9 26.6 + - - +
123B ARG* 4.7 8.3 - - - +
432B ARG 5.5 0.4 + - - -
433B ASP* 3.3 10.8 + - + +
435B PRO* 1.3 77.2 - - - +
437B ILE* 1.3 61.0 + - + +
440B GLY* 2.9 26.5 + - - -
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Residues in contact with ILE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLN* 3.8 38.1 - - + +
411B LEU* 4.6 2.9 - - + -
414B LEU* 4.3 28.7 - - + -
428B GLY 3.4 24.9 - - - +
429B TYR* 4.4 9.2 - - + -
433B ASP* 3.1 17.9 + - + +
434B LEU* 3.7 9.6 - - + +
436B ALA* 1.3 76.6 - - + +
438B GLU* 1.3 63.6 + - - +
440B GLY* 3.2 10.9 + - - -
441B LEU* 3.2 19.4 + - + +
510B PHE* 3.8 21.5 - - + -
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU 2.9 16.7 + - - +
435B PRO* 3.9 5.4 - - + +
437B ILE* 1.3 76.4 - - - +
439B GLY* 1.3 62.9 + - - +
441B LEU* 3.3 19.4 + - - +
442B LYS* 3.2 44.0 + - - +
507B LEU* 3.4 23.1 - - + +
510B PHE* 3.7 30.5 - - + -
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Residues in contact with GLY 439 (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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120B PRO* 3.8 19.2 - - - +
121B ASN* 3.3 23.1 - - - -
435B PRO 2.9 12.7 + - - -
438B GLU* 1.3 77.2 - - - +
440B GLY* 1.3 55.7 + - - +
442B LYS* 3.2 5.1 + - - +
443B GLN* 2.9 33.6 + - - +
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Residues in contact with GLY 440 (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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121B ASN* 3.4 9.3 - - - +
436B ALA 2.9 15.8 + - - -
437B ILE 3.2 3.8 + - - -
439B GLY* 1.3 76.2 - - - +
441B LEU* 1.3 57.5 + - - +
443B GLN* 3.4 6.6 + - - +
444B LEU* 3.0 30.7 + - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B SER* 4.2 11.2 - - - +
410B GLN* 4.2 16.6 - - - +
411B LEU* 3.6 39.5 - - + -
437B ILE* 3.2 15.6 + - + +
438B GLU* 3.6 7.4 - - - +
439B GLY 3.3 0.4 - - - -
440B GLY* 1.3 76.7 - - - +
442B LYS* 1.3 58.2 + - - +
444B LEU* 3.9 4.9 - - + +
503B THR* 4.0 3.6 - - - +
506B ARG* 2.9 59.3 + - + +
507B LEU* 3.8 15.3 - - + -
510B PHE* 3.8 24.7 - - + -
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Residues in contact with LYS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 4.6 16.8 - - + -
438B GLU* 3.2 41.6 + - - +
439B GLY* 3.2 5.8 + - - +
440B GLY 3.2 0.2 - - - -
441B LEU* 1.3 76.5 - - - +
443B GLN* 1.3 65.5 + - - +
444B LEU 3.3 0.2 - - - -
445B GLU* 3.2 24.1 + - - +
446B ARG* 4.5 1.7 + - - +
503B THR* 3.8 15.9 - - + -
507B LEU* 3.4 24.7 - - + +
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.7 42.5 - - + +
118B ALA 4.6 0.8 + - - -
119B GLY* 3.6 4.8 - - - -
120B PRO* 3.4 21.0 - - + +
121B ASN* 3.1 46.8 + - - +
122B ALA* 4.4 2.0 - - - +
439B GLY 2.9 17.8 + - - +
440B GLY* 3.9 5.8 - - - +
442B LYS* 1.3 77.2 - - - +
444B LEU* 1.3 61.1 + - - +
445B GLU 3.0 1.4 + - - -
446B ARG* 3.1 13.3 + - - -
447B ARG* 3.8 23.0 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA* 3.9 17.7 - - + +
404B MET* 4.0 14.8 - - + -
407B SER* 3.5 24.0 - - - +
440B GLY 3.0 18.4 + - - +
441B LEU* 3.9 8.5 - - - +
442B LYS 3.3 0.6 - - - -
443B GLN* 1.3 74.0 - - - +
445B GLU* 1.3 57.1 + - - +
447B ARG* 2.8 35.4 + - + +
448B TYR* 3.3 27.6 + - + +
506B ARG* 3.8 21.5 - - - +
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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