Contacts of the strand formed by residues 291 - 296 (chain H) in PDB entry 1OAK
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 291 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H THR* 4.0 9.5 - - + +
236H CYS 3.2 6.3 - - - +
237H THR* 3.7 29.2 + - + +
243H LEU* 3.5 1.9 - - - +
285H LYS* 3.1 3.6 - - - +
286H ASP 2.7 33.6 + - - -
289H LYS* 2.9 43.5 + - + +
290H SER* 1.3 79.3 - - - +
292H VAL* 1.3 63.7 + - - +
293H PHE* 3.8 27.5 - - + -
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Residues in contact with VAL 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234H ILE 3.8 0.7 - - - +
235H THR* 3.6 1.4 - - - -
236H CYS* 2.7 42.8 + - + +
238H VAL* 4.6 4.3 - - + -
243H LEU* 3.7 21.3 - - + -
248H VAL* 3.8 28.5 - - + -
250H TRP* 3.7 14.6 - - - +
265H ILE* 4.0 10.8 - - + -
283H ILE* 3.6 23.1 - - + -
284H THR 3.4 12.1 - - - +
285H LYS* 3.8 6.7 - - + -
291H GLN* 1.3 77.2 - - - +
293H PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234H ILE 3.6 3.8 - - - +
235H THR* 3.5 38.1 - - + -
282H SER 3.6 1.0 - - - +
283H ILE* 3.3 6.4 - - - +
284H THR* 2.6 61.0 + - - +
285H LYS* 3.8 22.7 - - - -
286H ASP* 3.8 13.0 - - + -
289H LYS* 4.2 10.8 - - - -
291H GLN* 3.8 26.7 - - + -
292H VAL* 1.3 75.5 - - - +
294H LEU* 1.3 62.1 - - - +
295H LYS* 5.5 1.5 - - + +
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Residues in contact with LEU 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H LEU* 3.8 35.2 - - + +
233H SER* 3.5 5.2 + - - -
234H ILE* 2.9 37.4 + - + +
250H TRP* 3.6 56.5 - - + +
262H LEU* 4.5 9.6 - - + -
281H LEU* 3.5 23.8 - - + -
282H SER 3.4 3.8 - - - -
283H ILE* 4.6 1.8 - - - +
292H VAL 4.1 0.4 + - - -
293H PHE* 1.3 76.7 - - - +
295H LYS* 1.3 72.8 + - - +
296H MET* 4.2 2.0 - - + +
307H TYR* 4.6 5.6 - - + -
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Residues in contact with LYS 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H SER* 3.4 26.2 - - - -
232H LEU 3.3 7.0 - - - +
233H SER* 3.3 22.4 + - - +
280H ARG 3.4 2.3 - - - +
281H LEU* 3.2 3.9 - - - +
282H SER* 2.8 55.8 + - - +
293H PHE* 5.5 1.3 - - + +
294H LEU* 1.3 77.4 - - - +
296H MET* 1.3 61.0 + - - +
297H ASN* 4.3 14.8 - - - +
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Residues in contact with MET 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H SER* 2.9 8.2 - - - -
232H LEU* 2.8 41.0 + - + -
252H ARG* 3.9 7.6 - - - +
262H LEU* 5.4 2.2 - - - -
277H LEU* 4.6 14.4 - - + -
280H ARG* 2.9 61.5 - - + +
281H LEU* 3.9 18.6 - - + -
294H LEU* 4.2 2.9 - - + +
295H LYS* 1.3 74.9 - - - +
297H ASN* 1.3 63.8 + - - +
299H LEU* 3.0 21.1 - - + +
303H ASP* 3.4 19.3 - - + +
307H TYR* 4.3 17.5 - - - +
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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