Contacts of the helix formed by residues 452 - 460 (chain B) in PDB entry 2W93
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 GLN 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A GLN 2.9 30.7 + - - +
449A LEU 3.1 14.3 + - - -
450A THR 3.8 0.6 - - - +
451A VAL* 4.0 7.6 - - + +
452A GLN* 2.9 43.1 + - - -
493A TRP* 3.8 16.4 - - + -
49B ALA* 3.6 15.9 - - + +
50B ASN* 3.5 13.1 + - - +
53B ASN* 3.3 13.7 + - - +
450B THR* 3.2 11.4 - - - -
451B VAL* 1.3 79.7 - - - +
453B GLU* 1.3 58.5 + - - +
454B ILE 3.1 0.4 - - - -
455B SER* 2.9 28.5 + - - -
502B PHE* 4.0 10.3 - - - -
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Residues in contact with GLU 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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48B ASN* 2.8 22.0 + - - +
49B ALA* 2.9 23.8 + - - +
53B ASN* 3.0 43.7 + - + +
419B THR* 4.1 15.0 - - + +
420B GLY* 4.6 4.5 - - - -
423B LEU* 3.9 21.5 - - + +
450B THR 3.0 10.2 + - - +
451B VAL 3.0 1.2 + - - -
452B GLN* 1.3 73.9 - - - +
454B ILE* 1.3 63.6 + - - +
455B SER 3.1 0.2 - - - -
456B THR* 2.7 32.0 + - - -
457B MET* 3.4 17.1 + - - +
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B THR* 4.2 11.8 - - + +
447B LEU* 4.0 20.4 - - + -
451B VAL* 3.1 23.3 + - + +
452B GLN 3.1 0.8 - - - -
453B GLU* 1.3 75.5 - - - +
455B SER* 1.3 62.4 + - - +
457B MET* 3.1 13.7 + - + +
458B ILE* 3.1 25.1 + - + +
466B LEU* 4.1 17.9 - - + -
498B LEU* 4.6 3.1 - - + -
499B LEU* 3.5 33.0 - - + +
502B PHE* 4.0 11.4 - - + -
533B ILE* 4.7 2.0 - - + -
535B MET* 3.8 27.1 - - + -
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Residues in contact with SER 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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448A GLN* 4.6 2.8 + - - -
491A GLN* 3.1 20.5 - - - +
493A TRP* 2.9 37.9 + - - -
49B ALA* 4.9 3.4 - - - +
452B GLN 2.9 17.5 + - - -
454B ILE* 1.3 79.3 - - - +
456B THR* 1.3 57.9 + - - +
458B ILE* 3.2 7.1 + - - +
459B ARG* 3.0 26.7 + - - +
502B PHE* 4.0 14.5 - - - -
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Residues in contact with THR 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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46B ALA* 3.4 28.9 - - + +
47B GLY 3.6 17.1 + - - +
48B ASN* 4.3 1.1 - - - +
49B ALA* 3.7 8.0 + - - +
423B LEU* 3.8 24.6 - - + +
453B GLU* 2.7 34.5 + - - +
455B SER* 1.3 74.0 + - - +
457B MET* 1.3 65.6 + - - +
459B ARG* 3.1 25.3 - - + +
460B TRP* 3.3 13.1 + - + +
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Residues in contact with MET 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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419B THR* 3.2 40.2 - - + +
422B THR* 4.0 10.8 - - + -
423B LEU* 3.5 32.1 - - + +
453B GLU 3.6 14.4 - - - +
454B ILE* 3.1 18.6 + - + +
456B THR* 1.3 79.7 - - - +
458B ILE* 1.3 61.3 + - - +
460B TRP 3.5 0.3 + - - -
461B GLY 3.2 2.8 + - - -
462B LEU* 3.0 40.7 + - + +
464B PRO* 3.8 23.1 - - + -
466B LEU* 4.3 9.6 - - + -
533B ILE* 3.8 17.3 - - + -
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Residues in contact with ILE 458 (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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491A GLN* 3.5 21.8 - - - +
454B ILE* 3.1 16.3 + - + +
455B SER* 3.2 5.8 + - - +
457B MET* 1.3 75.6 - - - +
459B ARG* 1.3 64.4 + - - +
461B GLY* 3.0 15.2 + - - +
462B LEU 5.4 0.7 - - - -
499B LEU* 3.7 22.4 - - + +
502B PHE* 3.7 30.3 - - + +
503B GLY 4.2 1.1 - - - +
504B ALA* 3.6 40.8 - - + -
505B LYS 4.9 1.3 - - - +
533B ILE* 4.5 10.5 - - + -
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Residues in contact with ARG 459 (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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486A GLN* 4.3 21.3 + - - +
489A GLU* 3.4 35.5 + - - +
490A ILE* 4.0 6.3 - - - +
491A GLN* 3.3 38.9 - - + +
46B ALA 3.5 17.4 + - - -
47B GLY* 3.0 33.3 + - - -
455B SER 3.0 10.2 + - - +
456B THR* 3.1 28.3 - - - +
458B ILE* 1.3 76.7 - - - +
460B TRP* 1.3 70.9 + - + +
461B GLY 3.8 0.5 + - - -
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Residues in contact with TRP 460 (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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486A GLN* 3.9 13.6 - - + +
44B ARG* 3.7 45.6 + - + +
45B TRP 3.3 21.5 - - - -
46B ALA* 2.8 25.9 + - - +
427B PHE* 3.4 33.7 - + + -
430B GLU* 4.4 6.6 - - - +
456B THR* 3.3 9.0 + - + +
458B ILE 3.2 0.4 - - - -
459B ARG* 1.3 107.6 - - + +
461B GLY* 1.3 64.9 + - - +
462B LEU* 3.2 12.9 + - + +
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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