Contacts of the helix formed by residues 320 - 330 (chain B) in PDB entry 1KHU
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 ASN 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LEU* 4.5 8.0 - - - +
318B ASN 4.6 3.6 - - - +
319B ARG* 1.3 79.4 - - - +
321B SER* 1.3 64.7 + - - +
322B THR* 3.4 18.4 - - + +
323B ILE* 2.8 43.8 - - - +
324B GLU* 2.8 18.2 + - - +
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Residues in contact with SER 321 (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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320B ASN* 1.3 71.9 - - - +
322B THR* 1.3 62.9 + - - +
324B GLU* 2.9 10.2 + - - +
325B ASN* 2.6 35.5 + - - +
328B ARG* 5.0 0.5 + - - -
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Residues in contact with THR 322 (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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320B ASN* 3.4 29.2 - - + +
321B SER* 1.3 80.6 + - - +
323B ILE* 1.3 61.2 + - + +
325B ASN* 3.3 9.3 + - - +
326B THR* 3.2 25.1 + - - -
418B LYS* 5.5 4.7 + - - -
433B PRO* 4.9 6.3 - - - +
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Residues in contact with ILE 323 (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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278B GLU* 3.6 42.4 - - + +
279B LEU* 3.3 35.2 - - + -
316B ASN* 4.8 0.9 - - - +
318B ASN 4.7 3.1 - - - +
319B ARG* 4.3 10.1 - - + +
320B ASN* 2.8 41.1 - - - +
322B THR* 1.3 73.9 - - + +
324B GLU* 1.3 64.6 + - - +
326B THR* 3.3 5.0 + - - -
327B ARG* 2.9 24.5 + - - +
433B PRO* 3.6 31.6 - - + +
434B CYS* 4.4 1.8 - - - -
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Residues in contact with GLU 324 (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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319B ARG* 3.1 30.3 + - + +
320B ASN 2.8 12.4 + - - +
321B SER* 3.2 12.6 - - - +
323B ILE* 1.3 76.6 - - - +
325B ASN* 1.3 68.7 + - - +
327B ARG* 3.1 30.2 + - - +
328B ARG* 3.2 40.4 + - - +
404C TYR* 4.0 15.9 + - - -
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Residues in contact with ASN 325 (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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321B SER 2.6 16.3 + - - +
322B THR* 3.4 14.4 - - - +
323B ILE 3.2 0.2 - - - -
324B GLU* 1.3 77.4 - - - +
326B THR* 1.3 64.9 + - - +
328B ARG* 2.9 35.0 + - - +
329B HIS* 3.6 25.9 + - - -
418B LYS* 5.5 5.4 + - - -
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Residues in contact with THR 326 (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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322B THR 3.2 11.9 + - - -
323B ILE 3.5 7.9 - - - -
325B ASN* 1.3 79.0 + - - +
327B ARG* 1.3 57.4 + - - +
329B HIS* 2.8 27.8 + - - +
330B ILE* 3.3 8.8 + - - +
416B PHE* 3.4 26.7 - - + +
417B VAL* 3.7 15.5 - - + -
418B LYS* 3.7 15.3 - - + +
433B PRO* 3.2 27.1 - - + +
434B CYS* 3.9 13.0 - - + -
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Residues in contact with ARG 327 (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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276B TYR* 3.5 11.5 + - - +
278B GLU* 3.1 24.5 + - - -
298B GLY* 5.1 6.4 - - - +
311B LEU* 2.9 27.8 + - - +
312B GLY* 3.0 32.6 + - - -
314B LEU 3.5 9.5 + - - -
319B ARG* 3.3 32.5 - - - +
323B ILE* 2.9 18.9 + - - +
324B GLU* 3.1 23.6 + - - +
326B THR* 1.3 74.7 - - - +
328B ARG* 1.3 62.5 + - - +
329B HIS 3.3 0.5 + - - -
330B ILE* 3.3 26.5 + - + +
331B GLY 4.7 0.9 + - - -
434B CYS* 3.5 16.6 - - - -
404C TYR* 4.0 13.7 + - - +
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Residues in contact with ARG 328 (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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321B SER 5.0 0.4 + - - -
324B GLU* 3.2 45.1 + - - +
325B ASN* 2.9 25.1 + - - +
327B ARG* 1.3 76.2 - - - +
329B HIS* 1.3 64.1 + - + +
330B ILE 3.4 0.6 + - - -
331B GLY* 4.5 4.6 + - - -
400C PHE* 5.5 9.1 - - + -
401C GLU* 5.4 13.3 + - - +
404C TYR* 3.8 34.1 - - + -
405C GLU* 5.4 5.3 + - - -
456C SER* 5.8 4.2 - - - -
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Residues in contact with HIS 329 (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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325B ASN* 3.6 41.3 + - - -
326B THR* 2.8 11.4 + - - +
328B ARG* 1.3 80.3 + - + +
330B ILE* 1.3 64.4 + - - +
331B GLY* 3.2 3.6 + - - -
349B SER* 3.1 15.2 + - - -
350B ASP* 4.8 2.3 + - - +
351B SER* 3.6 24.2 + - - +
417B VAL* 3.8 15.0 - - + -
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Residues in contact with ILE 330 (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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276B TYR* 4.8 3.1 - - + +
297B ASP 4.0 5.2 - - - -
298B GLY* 3.6 26.7 - - - +
311B LEU* 4.4 16.2 - - + -
326B THR 3.3 10.7 + - - +
327B ARG* 3.3 22.5 + - + +
329B HIS* 1.3 78.7 - - - +
331B GLY* 1.3 62.8 + - - +
333B GLY* 2.9 16.8 + - - -
349B SER* 3.1 13.8 - - - -
416B PHE* 3.9 54.7 - - + -
417B VAL* 5.0 1.1 - - + -
434B CYS* 4.0 20.4 - - + -
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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