Contacts of the helix formed by residues 407 - 413 (chain B) in PDB entry 1OL1
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 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ASP* 3.4 2.2 + - - -
401B ALA 3.2 13.3 + - - -
402B PRO 3.1 20.5 + - - +
404B HIS 2.6 26.4 + - - +
405B ALA 4.4 4.5 - - - +
406B GLN* 1.3 80.4 + - - +
408B SER* 1.3 69.1 + - - +
409B ILE 3.1 3.4 - - - -
410B ARG* 3.0 39.7 + - - +
411B GLU* 2.9 31.7 + - + +
414B LYS* 5.7 1.0 + - - -
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Residues in contact with SER 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASP* 2.5 48.9 + - - -
219B VAL* 3.8 12.1 - - - +
220B GLU* 3.9 22.0 + - - -
223B GLU* 5.6 0.7 - - - +
407B GLN* 1.3 78.5 - - - +
409B ILE* 1.3 62.8 + - - +
411B GLU* 3.4 6.9 + - - +
412B LYS* 3.2 22.9 + - - +
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Residues in contact with ILE 409 (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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216B ASP* 4.2 0.8 + - - +
219B VAL* 3.4 29.4 - - + -
335B PHE* 3.8 15.0 - - + -
338B GLU* 3.2 45.5 - - + +
339B LEU* 3.9 12.8 - - + +
342B ILE* 3.2 30.7 - - + -
407B GLN 3.1 0.8 - - - -
408B SER* 1.3 77.6 - - - +
410B ARG* 1.3 62.6 + - - +
412B LYS* 3.1 3.4 + - - +
413B TYR* 2.9 43.6 + - + -
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Residues in contact with ARG 410 (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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335B PHE* 3.6 19.9 - - + -
339B LEU* 5.3 3.0 - - + +
401B ALA* 4.0 21.3 - - + -
402B PRO* 3.3 43.4 + - - +
407B GLN* 3.0 37.8 + - - +
409B ILE* 1.3 80.2 - - - +
411B GLU* 1.3 58.1 + - + +
413B TYR 4.4 0.2 - - - +
414B LYS* 3.1 50.0 + - - +
422B SER* 3.2 40.6 + - - +
423B LEU* 5.4 5.1 - - - +
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Residues in contact with GLU 411 (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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407B GLN* 2.9 24.8 + - + +
408B SER* 3.9 6.5 - - - +
410B ARG* 1.3 77.7 - - + +
412B LYS* 1.3 62.4 + - - +
414B LYS* 2.8 46.3 + - - +
415B ASN* 4.3 4.3 + - - +
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Residues in contact with LYS 412 (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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219B VAL* 4.1 19.1 + - + +
222B GLY* 5.8 0.8 - - - -
223B GLU* 3.0 49.0 + - + +
229B ASN* 3.5 20.9 + - - +
232B LEU* 4.3 8.1 - - - +
338B GLU* 3.4 30.7 + - - +
408B SER 3.2 13.4 + - - +
409B ILE* 3.1 4.1 + - - +
411B GLU* 1.3 80.0 - - - +
413B TYR* 1.3 80.3 + - + +
414B LYS 3.2 4.4 + - - -
415B ASN* 3.5 12.5 + - - +
418B TYR* 3.4 25.6 - - + -
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Residues in contact with TYR 413 (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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229B ASN* 3.3 14.0 + - - -
331B SER 3.6 20.0 - - - -
334B MET* 3.7 13.4 - - + +
335B PHE* 3.5 44.4 - + + -
338B GLU* 2.7 43.3 + - - +
409B ILE* 2.9 29.4 + - + +
410B ARG 3.5 2.9 + - - -
412B LYS* 1.3 90.4 - - + +
414B LYS* 1.3 61.6 + - - +
415B ASN 3.4 2.4 - - - +
418B TYR* 3.7 32.9 - + - +
420B GLY* 3.7 8.3 - - - -
421B VAL* 3.7 9.0 - - + +
422B SER* 3.5 24.3 + - - -
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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