Contacts of the helix formed by residues 345 - 354 (chain B) in PDB entry 1O92
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 GLU 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341B LYS* 2.5 57.7 + - + +
342B THR* 2.8 21.5 + - + +
344B ARG* 1.3 78.7 - - - +
346B LEU* 1.3 61.5 + - - +
347B LEU 3.3 1.1 - - - -
348B GLU* 3.4 9.9 + - - +
349B VAL* 3.0 27.9 + - - +
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Residues in contact with LEU 346 (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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306B LEU* 5.0 9.9 - - + -
311B LEU* 3.6 59.7 - - + +
312B CYS* 4.9 2.5 - - + -
333B ILE* 4.6 13.0 - - + -
335B THR* 3.9 4.3 - - - +
339B SER* 3.8 15.3 - - - +
341B LYS* 3.9 18.4 - - + -
342B THR 3.5 5.9 + - - +
343B GLU* 3.1 29.6 - - - +
345B GLU* 1.3 78.9 - - - +
347B LEU* 1.3 59.1 + - - +
348B GLU 3.3 0.2 - - - -
349B VAL* 3.2 5.4 + - + +
350B VAL* 3.0 33.8 + - - +
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Residues in contact with LEU 347 (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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331B ILE* 3.6 53.8 - - + +
332B SER* 5.8 0.2 - - - -
333B ILE* 4.0 17.6 - - + +
343B GLU* 6.2 0.2 - - + -
344B ARG* 3.2 48.7 - - - +
345B GLU 3.3 1.4 - - - +
346B LEU* 1.3 80.4 - - - +
348B GLU* 1.3 54.7 + - - +
350B VAL* 3.2 4.0 + - + +
351B ASN* 2.7 49.5 + - - +
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Residues in contact with GLU 348 (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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344B ARG* 3.2 32.5 + - - +
345B GLU* 3.4 11.6 + - - +
346B LEU 3.3 0.4 - - - -
347B LEU* 1.3 75.8 - - - +
349B VAL* 1.3 59.7 + - + +
351B ASN* 3.3 12.4 + - - +
352B LYS* 2.9 78.7 + - + +
396B PHE 5.2 0.2 - - - -
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Residues in contact with VAL 349 (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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306B LEU* 5.5 0.9 - - + -
311B LEU* 3.8 22.7 - - + -
341B LYS* 4.1 23.6 - - + +
345B GLU 3.0 17.9 + - - +
346B LEU* 3.4 16.4 - - + +
347B LEU 3.2 0.2 - - - -
348B GLU* 1.3 78.7 - - + +
350B VAL* 1.3 58.4 + - + +
353B ASN* 2.9 53.7 + - - +
394B LEU* 4.6 5.6 - - + -
396B PHE* 4.0 26.9 - - - +
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Residues in contact with VAL 350 (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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302B VAL* 4.7 9.4 - - + -
306B LEU* 4.1 25.4 - - + -
331B ILE* 3.6 27.1 - - + -
333B ILE* 4.0 20.9 - - + -
346B LEU 3.0 16.3 + - - +
347B LEU* 3.5 7.9 - - + +
349B VAL* 1.3 77.7 - - - +
351B ASN* 1.3 61.2 + - - +
354B PHE* 2.8 53.9 + - + +
356B LEU* 4.8 2.9 - - + -
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Residues in contact with ASN 351 (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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328B PRO* 6.1 2.4 - - - +
331B ILE* 4.2 18.3 - - - +
344B ARG* 4.7 2.1 + - - -
347B LEU* 2.7 41.8 + - - +
348B GLU* 3.3 21.7 + - - +
350B VAL* 1.3 79.1 - - - +
352B LYS* 1.3 60.8 + - - +
353B ASN 3.5 0.2 - - - -
354B PHE 3.9 12.8 + - - +
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Residues in contact with LYS 352 (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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348B GLU* 2.9 54.6 + - + +
349B VAL 4.1 0.7 - - - +
350B VAL 3.2 0.2 - - - -
351B ASN* 1.3 78.9 - - - +
353B ASN* 1.3 70.4 + - - +
354B PHE 3.8 0.2 - - - -
396B PHE 4.7 12.8 - - - +
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Residues in contact with ASN 353 (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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349B VAL* 2.9 37.8 + - - +
352B LYS* 1.3 93.5 - - - +
354B PHE* 1.3 56.8 + - + +
392B LYS* 2.6 39.7 + - + +
394B LEU* 3.1 53.0 - - + +
395B VAL* 3.4 16.5 + - - +
396B PHE 3.8 5.6 + - - +
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Residues in contact with PHE 354 (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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301B TRP* 3.8 30.5 - + - -
302B VAL* 3.7 34.1 - - + -
305B SER* 3.6 24.2 - - - -
306B LEU* 4.5 7.2 - - + -
350B VAL* 2.8 38.5 + - + +
351B ASN* 3.9 14.7 + - - +
352B LYS 3.8 0.4 - - - -
353B ASN* 1.3 85.7 - - + +
355B ASP* 1.3 60.9 + - - +
356B LEU* 3.7 15.6 + - + +
392B LYS* 3.5 23.3 - - + +
394B LEU* 3.4 28.3 - - + -
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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