Contacts of the helix formed by residues 283 - 292 (chain B) in PDB entry 3K72
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 GLY 283 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A HIS* 5.4 1.2 - - - +
465A TYR* 3.7 30.5 - - - -
469A ARG* 3.3 37.6 + - - -
499A TRP* 3.8 0.7 + - - -
281B SER* 3.2 4.3 + - - -
282B VAL* 1.3 81.1 - - - +
284B GLN* 1.3 56.2 + - - +
285B LEU 3.1 9.8 + - - -
286B ALA 3.9 6.0 + - - -
287B HIS* 3.9 1.4 + - - +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A TRP* 3.4 43.4 - - + +
219B MET* 3.5 19.3 - - + +
260B ASN* 3.1 53.3 + - - +
261B ASP 4.2 4.8 + - - -
280B PRO* 4.5 2.5 - - + -
281B SER* 3.1 36.2 + - - +
283B GLY* 1.3 76.5 - - - +
285B LEU* 1.3 60.1 + - - +
288B LYS* 3.4 21.5 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 4.0 29.8 - - + +
218B MET* 4.1 25.8 - - + -
219B MET* 3.4 37.2 - - + +
280B PRO* 4.7 4.0 - - + -
281B SER 4.5 7.4 - - - +
282B VAL* 4.3 12.8 - - - +
283B GLY 3.1 0.2 - - - -
284B GLN* 1.3 80.1 - - - +
286B ALA* 1.3 56.8 + - - +
287B HIS 2.5 16.6 + - - -
289B LEU* 2.7 46.4 + - + +
315B ILE* 4.3 10.1 - - + -
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Residues in contact with ALA 286 (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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465A TYR* 3.6 24.2 - - + +
469A ARG* 4.5 8.1 - - - +
282B VAL 4.7 2.5 + - - +
283B GLY* 3.9 3.8 + - - +
285B LEU* 1.3 77.7 - - - +
287B HIS* 1.3 54.7 + - - +
290B ALA* 3.1 24.5 - - - +
314B ILE* 5.2 0.4 - - + -
315B ILE* 3.7 33.6 - - + +
316B PRO* 4.2 11.5 - - + +
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Residues in contact with HIS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A ARG* 3.1 30.5 - - - +
499A TRP* 3.7 33.0 - + + -
283B GLY 3.9 2.5 + - - +
285B LEU 2.5 5.8 + - - -
286B ALA* 1.3 74.9 - - - +
288B LYS* 1.3 75.5 + - + +
290B ALA* 3.4 1.4 + - - +
291B GLU* 2.9 44.5 + - + +
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Residues in contact with LYS 288 (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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499A TRP* 4.9 5.8 - - + -
219B MET* 3.6 19.7 - - + +
222B ALA 3.9 15.3 + - - +
223B ALA* 4.1 9.5 + - - +
262B GLY* 2.6 35.9 + - - -
263B ARG* 4.8 4.2 - - - +
284B GLN 3.4 18.4 + - - +
285B LEU 3.2 0.8 + - - -
287B HIS* 1.3 85.4 - - + +
289B LEU* 1.3 66.2 + - - +
291B GLU* 3.1 31.9 + - - +
292B ASN* 3.2 29.5 + - - +
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Residues in contact with LEU 289 (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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218B MET* 5.4 9.9 - - + +
219B MET* 5.4 0.8 - - - -
222B ALA* 4.9 8.7 - - + -
237B LEU* 5.2 3.6 - - + -
285B LEU* 2.7 36.9 + - + +
286B ALA* 4.9 0.2 - - - -
288B LYS* 1.3 75.6 - - - +
290B ALA* 1.3 58.4 + - - +
291B GLU 3.0 1.2 + - - -
292B ASN* 3.1 14.3 + - - +
294B ILE* 3.2 64.6 + - + +
295B GLN* 4.4 2.2 - - - +
296B PRO* 3.3 33.7 - - + -
315B ILE* 3.6 25.6 - - + -
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Residues in contact with ALA 290 (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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285B LEU 3.5 1.2 + - - -
286B ALA* 3.1 25.1 - - - +
287B HIS 3.4 2.1 + - - +
289B LEU* 1.3 79.8 - - + +
291B GLU* 1.3 59.6 + - - +
292B ASN 3.4 0.2 - - - -
293B ASN* 3.6 16.9 + - - +
294B ILE 4.3 0.9 - - - +
295B GLN* 3.8 21.8 - - - +
315B ILE* 6.1 0.4 - - + -
316B PRO* 5.2 8.1 - - + -
317B LYS* 5.0 7.4 - - - +
407B ARG* 4.4 8.1 + - - -
409B LEU* 5.5 8.5 - - - -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B HIS* 2.9 32.6 + - + +
288B LYS* 3.2 29.1 - - - +
289B LEU 3.0 0.4 - - - -
290B ALA* 1.3 79.3 - - - +
292B ASN* 1.3 64.3 + - - +
293B ASN* 3.2 11.7 + - - +
407B ARG* 5.2 4.1 + - - +
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Residues in contact with ASN 292 (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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222B ALA* 3.1 33.9 + - + +
223B ALA* 5.1 1.6 + - - +
235B ARG* 3.4 36.3 + - - +
288B LYS* 3.7 23.4 + - - +
289B LEU 3.1 7.3 + - - +
291B GLU* 1.3 89.3 - - - +
293B ASN* 1.3 73.3 + - - +
294B ILE* 3.2 11.5 + - + +
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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