Contacts of the helix formed by residues 285 - 290 (chain H) in PDB entry 3KDO
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 HIS 285 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ASN* 6.0 2.2 - - - -
114A GLY* 5.7 3.2 - - - -
257H VAL* 4.1 12.1 - - + +
282H ARG* 2.6 82.0 + - + +
283H ALA* 3.4 1.3 + - - -
284H MET* 1.3 75.1 - - - +
286H ALA* 1.3 68.7 + - + +
287H ALA 2.6 17.4 + - - -
288H PHE* 2.7 28.1 + - - -
289H THR* 2.6 46.0 + - + +
298H MET* 4.7 1.7 - - + -
301H LEU* 4.4 6.5 - - + -
323H LEU* 6.2 0.2 - - - +
324H GLU 6.0 1.1 - - - -
600H CAP 4.2 7.1 + - - -
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Residues in contact with ALA 286 (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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111A ASN 6.0 0.4 - - - -
113A PHE* 3.4 36.6 - - + +
114A GLY* 3.4 12.6 - - - +
294A HIS* 2.8 21.1 + - - -
284H MET 3.4 0.4 - - - -
285H HIS* 1.3 90.4 + - + +
287H ALA* 1.3 59.3 + - - +
288H PHE 3.0 2.2 + - - -
289H THR* 3.4 11.9 - - - -
290H ARG* 3.4 19.7 + - + +
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Residues in contact with ALA 287 (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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113A PHE* 3.8 21.4 - - + +
287A ALA 4.1 0.7 - - - +
288A PHE* 3.2 26.5 - - + +
294A HIS* 4.0 14.3 - - - +
295A GLY* 3.7 23.9 - - - -
296A ILE* 4.6 6.3 - - + -
284H MET* 3.2 19.4 + - + +
285H HIS 2.6 5.3 + - - -
286H ALA* 1.3 75.9 - - - +
288H PHE* 1.3 59.0 + - + +
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Residues in contact with PHE 288 (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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287A ALA* 3.3 25.4 - - + +
288A PHE* 4.0 23.6 - + + -
122H ARG* 4.9 0.2 + - - -
257H VAL* 3.9 25.6 - - + -
261H TRP* 6.5 0.2 - + - -
284H MET* 4.2 7.9 - - + -
285H HIS* 2.7 13.8 + - - -
286H ALA 4.1 0.2 - - - -
287H ALA* 1.3 82.7 - - + +
289H THR* 1.3 77.9 + - + +
290H ARG 3.5 2.2 - - - -
291H ASN* 4.9 1.3 - - - +
294H HIS 3.7 6.7 - - - +
295H GLY* 3.4 6.2 - - - -
296H ILE* 2.8 57.0 + - + +
301H LEU* 3.8 25.8 - - + -
305H TYR* 5.9 0.2 - - - -
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Residues in contact with THR 289 (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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122H ARG* 3.2 18.8 + - - +
285H HIS* 2.6 45.0 + - + +
286H ALA* 3.4 3.1 - - - -
288H PHE* 1.3 109.3 - - + +
290H ARG* 1.3 59.4 + - - +
291H ASN 3.7 0.7 - - - -
296H ILE 3.1 14.1 - - - +
298H MET* 4.0 23.4 + - + +
301H LEU* 4.1 6.7 - - + -
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Residues in contact with ARG 290 (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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113A PHE 2.9 28.2 + - - -
114A GLY* 2.9 26.2 - - - -
115A MET 3.1 19.5 + - - -
116A LYS* 3.8 9.3 + - - +
118A VAL* 3.5 15.8 + - - +
119A LYS* 4.8 11.0 + - - +
294A HIS* 4.2 12.5 - - + +
122H ARG* 4.3 1.6 + - - -
286H ALA* 3.4 21.0 + - - +
288H PHE 3.5 0.6 - - - -
289H THR* 1.3 80.5 + - - +
291H ASN* 1.3 62.1 + - - +
292H PRO* 3.1 13.7 - - - +
324H GLU* 3.6 30.6 - - + +
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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