Contacts of the helix formed by residues 448 - 457 (chain B) in PDB entry 2WK6
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 SER 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446B ALA 3.5 2.0 + - - -
447B LEU* 1.3 73.5 - - - +
449B GLY* 1.3 56.2 + - - +
450B PRO* 3.5 12.5 - - - +
451B GLN* 2.7 40.6 + - - +
452B SER* 2.7 36.3 + - - -
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Residues in contact with GLY 449 (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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448B SER* 1.3 77.1 - - - +
450B PRO* 1.3 70.6 - - - +
451B GLN 2.9 1.4 + - - -
452B SER* 2.9 4.6 + - - -
453B ARG* 2.9 32.1 + - - +
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Residues in contact with PRO 450 (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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448B SER* 3.5 12.3 - - - +
449B GLY* 1.3 84.9 - - - +
451B GLN* 1.3 59.7 + - + -
453B ARG* 3.6 24.7 + - - +
454B ALA* 3.1 24.4 + - - +
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Residues in contact with GLN 451 (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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400B VAL* 4.1 15.4 - - + +
403B GLU* 3.2 34.9 + - - +
404B LEU* 3.4 29.5 - - - +
446B ALA 4.1 3.1 - - - +
447B LEU* 3.5 12.6 - - + -
448B SER* 2.7 47.8 + - - +
449B GLY 3.0 1.2 - - - -
450B PRO* 1.3 78.1 - - + +
452B SER* 1.3 63.9 + - - +
454B ALA* 3.4 5.8 + - - +
455B LEU* 3.1 29.5 + - - +
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Residues in contact with SER 452 (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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379B GLU* 4.8 2.3 + - - -
381B LEU* 4.9 11.1 - - - +
447B LEU* 3.8 23.1 + - - +
448B SER 2.7 24.2 + - - -
449B GLY* 3.6 4.9 - - - -
451B GLN* 1.3 70.0 - - - +
453B ARG* 1.3 62.1 + - - +
455B LEU* 3.3 5.4 + - - +
456B GLN* 2.9 38.2 + - - +
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Residues in contact with ARG 453 (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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449B GLY* 2.9 23.2 + - - +
450B PRO* 3.6 24.5 + - - +
452B SER* 1.3 76.8 - - - +
454B ALA* 1.3 60.0 + - - +
456B GLN* 3.3 7.3 + - - +
457B GLU* 2.9 49.0 + - - +
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Residues in contact with ALA 454 (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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396B PRO* 3.7 18.8 - - + +
400B VAL* 3.8 18.4 - - + -
450B PRO 3.1 18.3 + - - +
451B GLN* 3.6 5.2 - - - +
453B ARG* 1.3 82.0 - - - +
455B LEU* 1.3 61.4 + - - +
457B GLU* 3.6 7.1 + - - +
458B ALA 3.4 12.8 + - - -
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Residues in contact with LEU 455 (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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381B LEU* 3.5 27.1 - - + -
396B PRO 4.1 1.3 - - - +
397B LEU* 3.8 34.5 - - + -
400B VAL* 3.7 35.2 - - + -
401B LEU* 4.7 2.0 - - + -
437B TRP* 3.0 13.4 - - - -
438B LEU* 4.0 3.6 - - + -
440B VAL* 3.9 23.1 - - + -
447B LEU* 3.9 13.9 - - + -
451B GLN 3.1 17.6 + - - +
452B SER* 3.8 2.0 - - - +
453B ARG 3.3 0.2 - - - -
454B ALA* 1.3 73.5 - - - +
456B GLN* 1.3 67.6 + - - +
458B ALA* 2.9 21.2 - - + +
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Residues in contact with GLN 456 (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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381B LEU* 4.3 14.9 - - + +
382B LEU 3.5 15.6 + - - +
384B PRO* 3.6 31.4 - - + +
437B TRP* 3.1 27.9 + - - +
452B SER* 2.9 30.8 + - - +
453B ARG* 3.6 6.7 - - - +
455B LEU* 1.3 71.6 - - - +
457B GLU* 1.3 60.9 + - - +
458B ALA 2.7 14.8 + - - -
459B LEU* 2.7 25.8 + - - +
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Residues in contact with GLU 457 (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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393B ARG* 3.6 24.9 + - - +
453B ARG* 2.9 37.0 + - - +
454B ALA* 3.9 8.3 - - - +
456B GLN* 1.3 81.3 - - - +
458B ALA* 1.3 58.3 + - - +
459B LEU 3.3 5.2 - - - +
460B VAL* 4.6 5.2 - - - +
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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