Contacts of the strand formed by residues 284 - 289 (chain A) in PDB entry 3HO5
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 LEU 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL* 3.5 23.0 - - - +
245A LEU* 3.8 27.1 - - + -
246A GLU 3.3 24.9 - - - +
247A LYS* 3.0 10.8 + - - +
249A GLY* 4.0 10.8 - - - -
250A TYR 3.6 23.8 - - - +
251A VAL* 4.3 9.4 - - + -
266A LEU* 5.5 0.7 - - + -
268A ILE* 5.0 9.9 - - + -
272A VAL* 3.8 2.3 - - + +
283A GLY* 1.3 71.8 - - - -
285A LEU* 1.3 63.7 + - - +
286A SER 4.5 4.9 - - - +
287A LEU* 6.1 0.2 - - + -
301A VAL* 3.4 33.0 - - + -
302A SER 4.0 2.5 - - - +
303A TYR* 4.1 11.7 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 3.7 18.8 - - - +
245A LEU* 4.3 2.7 - - - +
247A LYS* 6.0 0.9 - - - -
281A GLU* 3.5 25.1 - - + +
283A GLY 3.4 21.8 - - - +
284A LEU* 1.3 76.9 - - - +
286A SER* 1.3 65.8 + - - +
302A SER* 3.0 19.0 + - - +
303A TYR* 4.2 3.8 - - - -
304A THR* 4.0 12.3 - - - +
319A LEU* 3.6 32.5 - - + -
353A LEU* 4.8 5.2 - - + -
354A GLY 3.4 27.4 - - - +
355A GLY* 4.4 4.3 - - - -
356A GLN* 5.5 0.5 + - - -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.8 10.8 - - - +
284A LEU* 4.7 0.9 - - - +
285A LEU* 1.3 83.1 - - - +
287A LEU* 1.3 69.6 + - - +
300A TYR 3.9 0.4 - - - +
301A VAL* 3.4 7.7 - - - +
302A SER* 2.9 41.0 + - - +
355A GLY 3.3 12.6 - - - -
356A GLN* 3.7 9.1 - - - +
357A LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.4 22.2 - - + +
243A PHE* 4.6 0.2 - - + -
245A LEU* 3.6 24.2 - - + +
251A VAL* 3.7 38.1 - - + -
265A TYR* 5.0 0.7 - - + -
284A LEU* 6.2 0.2 - - + -
286A SER* 1.3 82.0 + - - +
288A ALA* 1.3 81.7 + - - +
289A PHE* 3.9 27.1 - - + -
299A LEU* 4.1 25.1 - - + -
300A TYR 3.3 15.9 - - - +
301A VAL* 4.1 10.3 - - + -
357A LEU* 4.4 3.4 - - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.1 6.5 - - + -
287A LEU* 1.3 75.6 - - - +
289A PHE* 1.3 64.0 + - - +
299A LEU* 3.6 1.4 - - - -
300A TYR* 2.8 46.3 + - + +
357A LEU* 3.8 33.4 - - + +
358A LEU* 4.3 7.4 - - - +
359A PHE* 4.6 6.5 - - + +
365A LEU* 4.5 10.8 - - + -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.9 26.4 - - + +
234A HIS 3.3 22.4 - - - +
235A SER* 3.8 24.2 - - - +
243A PHE* 3.6 38.8 - + - -
265A TYR* 3.6 24.7 - + - -
287A LEU* 3.9 15.9 - - + -
288A ALA* 1.3 76.6 - - - +
290A HIS* 1.3 64.0 + - - +
291A PRO* 3.6 0.9 - - - +
293A TYR* 3.5 30.1 - + + -
298A LYS 3.9 2.7 - - - -
299A LEU* 4.4 6.7 - - + -
359A PHE* 3.2 19.0 - - - +
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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