Contacts of the helix formed by residues 278 - 283 (chain B) in PDB entry 1K3B
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 PHE 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ASP* 3.3 39.5 - - - -
63A ILE* 4.3 16.6 - - + -
64A TYR* 3.4 44.9 - + + -
66A GLN* 3.4 31.2 - - + -
80A PHE* 5.8 1.6 - + - -
235B TYR* 3.9 5.5 - - - -
270B TYR 5.2 1.4 + - - -
271B ALA* 5.0 0.8 - - - +
272B GLN* 5.5 0.7 - - - -
277B GLY* 1.3 79.6 - - - -
279B PRO* 1.4 65.5 - - + +
280B TYR 4.5 0.4 - - - +
281B LEU* 2.9 33.4 + - + +
282B ILE* 3.2 13.6 + - - +
500B CL 3.6 20.6 - - + -
379C THR* 5.2 3.6 - - - -
429C ILE* 4.8 4.0 - - + -
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Residues in contact with PRO 279 (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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235B TYR* 3.9 21.7 - - + +
238B ALA* 4.5 0.7 - - + -
239B SER* 3.3 17.5 - - - +
277B GLY 4.3 0.4 - - - +
278B PHE* 1.4 84.3 - - + +
280B TYR* 1.3 58.5 + - - +
283B ALA* 2.7 30.6 + - + +
284B GLY 3.3 3.1 + - - -
347B ALA* 3.6 32.3 - - + -
348B VAL 5.5 1.6 - - - +
349B ALA* 6.1 2.7 - - + -
500B CL 3.6 13.2 - - + -
382C ALA* 4.1 20.2 - - + -
431C VAL* 4.2 9.4 - - + -
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Residues in contact with TYR 280 (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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61A THR* 3.6 18.6 - - + +
63A ILE* 4.0 30.3 - - + -
69A GLU* 2.5 36.7 + - + +
278B PHE 3.2 1.2 + - - -
279B PRO* 1.3 79.2 - - - +
281B LEU* 1.3 62.3 + - + +
284B GLY* 3.3 5.8 - - - +
285B LYS 3.1 21.0 + - - -
321B TYR* 3.8 24.3 + + - -
322B HIS* 4.1 7.6 - - - -
323B TYR* 3.5 55.0 - + + +
500B CL 3.2 19.3 - - + +
431C VAL* 3.8 13.6 - - + +
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Residues in contact with LEU 281 (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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63A ILE* 3.7 33.7 - - + -
78A PHE* 3.5 44.9 - - + -
80A PHE* 3.7 14.4 - - + -
270B TYR* 3.5 33.0 - - + +
278B PHE* 2.9 18.4 + - + +
280B TYR* 1.3 80.5 - - + +
282B ILE* 1.3 61.5 + - + +
285B LYS* 3.9 22.4 - - + -
286B TYR* 2.8 28.0 + - - +
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Residues in contact with ILE 282 (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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235B TYR* 3.8 20.9 - - + -
236B SER* 4.8 2.9 - - - -
239B SER* 3.6 22.4 - - - +
240B MET* 3.9 5.6 - - + -
264B VAL* 3.7 37.2 - - + -
268B SER* 3.4 25.4 - - - +
270B TYR* 4.2 4.3 - - + -
271B ALA* 3.9 13.2 - - + -
278B PHE 3.2 11.4 + - - +
279B PRO 3.1 1.4 + - - -
281B LEU* 1.3 85.8 - - + +
283B ALA* 1.3 69.1 + - - +
284B GLY 3.0 1.1 - - - -
286B TYR* 3.8 7.7 - - + +
287B ALA* 3.0 25.1 + - - +
292B LEU* 4.7 2.5 - - + +
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Residues in contact with ALA 283 (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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239B SER* 3.3 27.3 + - - +
242B MET* 3.3 34.5 - - + -
243B LEU* 3.8 12.1 - - + +
279B PRO* 2.7 16.1 + - + +
282B ILE* 1.3 75.2 - - - +
284B GLY* 1.3 57.4 + - - +
287B ALA* 3.2 4.3 - - - +
292B LEU* 5.4 0.2 - - - -
318B SER* 2.9 24.4 + - - -
431C VAL* 5.1 0.4 - - + -
433C ALA* 3.3 8.2 - - + +
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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