Contacts of the helix formed by residues 251 - 262 (chain B) in PDB entry 1KNU
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 ASP 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B ILE* 4.4 0.7 - - - +
250B TYR* 1.3 100.1 - - + +
252B MET* 1.3 66.3 + - + +
253B ASN* 3.2 12.4 + - - +
254B SER* 2.5 51.1 + - - -
255B LEU* 3.1 6.6 + - - +
352B PHE* 3.7 12.6 - - - -
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Residues in contact with MET 252 (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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251B ASP* 1.3 73.7 - - + +
253B ASN* 1.3 62.4 + - - +
255B LEU* 3.4 6.3 + - - +
256B MET* 3.4 32.1 + - + +
277B VAL* 3.9 42.2 - - + -
352B PHE* 3.6 19.5 - - + -
355B SER 5.8 3.8 - - - +
356B LEU* 5.9 3.8 - - + -
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Residues in contact with ASN 253 (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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250B TYR* 6.0 0.7 - - - +
251B ASP* 3.1 14.3 + - - +
252B MET* 1.3 78.9 - - - +
254B SER* 1.3 62.4 + - - +
256B MET* 3.2 21.9 + - - +
257B MET* 3.1 20.5 + - - +
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Residues in contact with SER 254 (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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247B PHE* 3.6 8.1 - - - -
248B VAL 3.9 13.0 - - - -
249B ILE* 3.6 2.3 - - - -
250B TYR* 3.0 32.2 + - - -
251B ASP* 2.5 47.9 + - - -
253B ASN* 1.3 69.9 - - - +
255B LEU* 1.3 53.8 + - - +
257B MET* 3.1 10.1 + - - +
258B GLY* 2.7 34.0 + - - -
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Residues in contact with LEU 255 (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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249B ILE* 3.7 35.4 - - + +
251B ASP 3.1 8.3 + - - +
252B MET* 3.6 11.4 - - - +
253B ASN 3.3 0.2 - - - -
254B SER* 1.3 76.8 + - - +
256B MET* 1.3 55.5 - - - +
258B GLY* 3.0 1.4 + - - -
259B GLU* 2.8 40.1 + - - +
264B PHE* 5.2 8.3 - - + -
277B VAL* 3.5 32.5 - - + -
280B ARG* 4.0 17.9 - - - +
281B ILE* 4.3 13.9 - - + -
348B MET* 4.3 13.0 - - + -
352B PHE* 4.3 6.7 - - + -
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Residues in contact with MET 256 (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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252B MET* 3.4 20.2 + - + +
253B ASN* 3.3 23.8 - - - +
255B LEU* 1.3 82.3 - - - +
257B MET* 1.3 61.2 + - - +
259B GLU* 3.5 11.2 + - - +
260B ASP* 3.0 28.7 - - - +
280B ARG* 6.0 2.0 - - - +
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Residues in contact with MET 257 (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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247B PHE* 3.9 15.7 - - + -
253B ASN* 3.1 11.2 + - - +
254B SER* 3.1 11.3 + - - +
256B MET* 1.3 79.2 - - - +
258B GLY* 1.3 60.1 + - - +
260B ASP* 2.9 12.8 + - + +
261B LYS* 2.8 62.0 + - - +
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Residues in contact with GLY 258 (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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247B PHE* 3.4 28.0 - - - -
249B ILE* 4.6 5.6 - - - -
254B SER 2.7 14.5 + - - -
255B LEU 3.5 3.6 - - - -
257B MET* 1.3 69.2 - - - +
259B GLU* 1.3 56.8 + - - +
260B ASP 3.0 5.2 - - - -
261B LYS* 4.1 3.4 - - - -
262B ILE* 2.8 31.2 + - - +
264B PHE* 3.4 12.2 - - - -
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Residues in contact with GLU 259 (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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255B LEU* 2.8 22.3 + - + +
256B MET* 3.6 11.4 - - - +
258B GLY* 1.3 76.2 - - - +
260B ASP* 1.3 61.4 + - - +
262B ILE 3.3 10.5 - - - +
263B LYS 4.4 5.5 - - - +
264B PHE* 3.6 14.1 - - + -
266B HIS* 6.0 0.5 - - - -
267B ILE* 3.4 38.5 - - + +
280B ARG* 3.2 39.1 + - - +
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Residues in contact with ASP 260 (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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256B MET* 3.0 20.5 - - - +
257B MET* 2.9 11.6 + - + +
259B GLU* 1.3 89.0 - - - +
261B LYS* 1.3 68.4 + - + +
262B ILE 4.1 1.7 - - - +
263B LYS* 5.5 0.7 - - - -
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Residues in contact with LYS 261 (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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247B PHE* 3.9 25.1 - - + -
257B MET* 2.8 57.4 + - - +
258B GLY* 3.9 4.3 - - - +
260B ASP* 1.3 82.3 - - + +
262B ILE* 1.3 67.4 + - + +
263B LYS* 3.7 1.7 + - - -
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Residues in contact with ILE 262 (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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247B PHE* 4.6 15.9 - - + -
249B ILE* 5.5 0.9 - - + -
258B GLY* 2.8 22.1 + - - +
259B GLU 3.3 14.6 - - - +
260B ASP 4.0 1.5 - - - -
261B LYS* 1.3 81.2 - - + +
263B LYS* 1.3 67.7 + - + +
264B PHE* 3.5 42.5 - - + +
341B ILE* 4.1 0.7 - - + -
342B SER* 3.6 24.2 - - - +
345B GLN* 3.8 32.1 - - + +
346B GLY* 3.9 24.2 - - - +
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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