Contacts of the helix formed by residues 426 - 435 (chain B) in PDB entry 4OSI
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 THR 426 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B GLY 3.9 3.2 - - - +
425B LEU* 1.3 74.2 - - - +
427B PRO* 1.3 62.2 - - - -
428B GLN* 2.5 46.8 + - - +
429B GLN* 2.5 36.5 + - + +
430B VAL 3.6 0.2 + - - -
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Residues in contact with PRO 427 (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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389B HIS 5.5 4.5 - - - +
390B GLY 5.7 1.6 - - - +
391B LEU* 3.9 25.4 - - + -
395B GLN* 5.6 0.4 - - - +
416B LEU* 4.2 9.4 - - + -
420B CYS* 3.9 21.3 - - + -
425B LEU 3.0 5.9 - - - +
426B THR* 1.3 85.0 - - - +
428B GLN* 1.3 70.1 + - - +
430B VAL* 2.9 4.5 + - + +
431B VAL* 2.9 33.4 + - - +
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Residues in contact with GLN 428 (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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395B GLN* 4.6 18.4 + - - +
426B THR* 2.5 35.7 + - - +
427B PRO* 1.3 88.2 - - - +
429B GLN* 1.3 56.6 + - + +
431B VAL* 3.7 7.7 + - - +
432B ALA* 2.9 26.3 + - - +
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Residues in contact with GLN 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLY 4.5 0.3 - - - +
425B LEU* 2.5 44.2 - - + +
426B THR* 2.5 32.5 + - - +
428B GLN* 1.3 72.5 - - + +
430B VAL* 1.3 58.5 + - - +
432B ALA* 3.2 9.3 + - + +
433B ILE* 2.9 36.0 + - - +
461B PRO* 5.3 0.7 - - - +
462B GLN* 4.4 20.4 - - - +
465B VAL* 4.0 32.1 - - + +
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Residues in contact with VAL 430 (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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412B VAL* 3.7 24.0 - - + -
415B LEU 5.6 0.2 - - - -
416B LEU* 3.9 24.2 - - + +
419B LEU* 4.2 19.5 - - + -
420B CYS* 4.0 13.2 - - - -
425B LEU* 3.5 33.0 - - + +
427B PRO 2.9 7.1 + - - +
429B GLN* 1.3 75.4 - - - +
431B VAL* 1.3 60.7 + - + +
433B ILE* 3.1 11.3 + - + +
434B ALA* 2.9 28.5 + - - +
443B LEU* 3.8 9.4 - - + +
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Residues in contact with VAL 431 (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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391B LEU* 3.8 31.0 - - + -
395B GLN* 4.0 40.8 - - + +
398B ALA* 5.1 1.8 - - + -
399B ILE* 4.2 21.0 - - + +
412B VAL* 5.6 0.9 - - + -
416B LEU* 5.7 0.9 - - + -
427B PRO 2.9 18.4 + - - +
428B GLN* 3.9 7.0 - - - +
430B VAL* 1.3 76.4 - - + +
432B ALA* 1.3 54.0 + - - +
434B ALA 3.3 0.9 + - - -
435B SER* 2.4 47.5 + - - +
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Residues in contact with ALA 432 (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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428B GLN 2.9 20.0 + - - +
429B GLN* 3.3 11.7 - - + +
430B VAL 3.2 0.4 - - - -
431B VAL* 1.3 77.6 - - - +
433B ILE* 1.3 58.0 + - - +
435B SER* 3.7 6.6 + - - -
436B ASN* 3.5 18.7 - - - +
465B VAL* 5.0 3.1 - - + -
469B SER* 3.6 20.6 + - - +
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Residues in contact with ILE 433 (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 LEU* 5.9 1.6 - - + -
425B LEU* 5.4 4.7 - - + -
429B GLN* 2.9 27.5 + - + +
430B VAL* 3.1 11.2 + - + +
432B ALA* 1.3 78.3 - - - +
434B ALA* 1.3 61.4 + - - +
435B SER 3.6 0.3 + - - -
436B ASN* 4.2 10.2 + - - +
439B GLY 4.6 0.7 + - - +
442B ALA* 3.6 34.9 - - + +
443B LEU* 3.7 23.1 - - + +
446B VAL* 4.4 17.9 - - + -
465B VAL* 4.1 24.2 - - + -
468B ALA* 3.8 27.7 - - + +
469B SER* 3.9 11.7 - - - +
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Residues in contact with ALA 434 (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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399B ILE* 3.9 32.3 - - + +
402B ASN* 4.0 1.0 + - - -
408B ALA* 4.0 11.1 - - + +
412B VAL* 3.8 13.0 - - + -
430B VAL 2.9 15.1 + - - +
431B VAL 3.3 3.1 + - - +
433B ILE* 1.3 74.9 - - - +
435B SER* 1.3 55.8 + - - +
436B ASN 3.1 14.8 + - - +
439B GLY* 4.8 3.6 - - - -
443B LEU* 3.6 27.8 - - + -
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Residues in contact with SER 435 (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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398B ALA* 4.2 18.9 - - - +
399B ILE* 4.0 6.4 - - - +
402B ASN* 3.2 22.1 + - - +
431B VAL* 2.4 36.4 + - - +
432B ALA* 3.7 9.1 + - - -
433B ILE 3.3 1.8 - - - -
434B ALA* 1.3 76.4 - - - +
436B ASN* 1.3 67.8 + - - +
4H G 6.0 1.8 - - - -
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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