Contacts of the helix formed by residues 315 - 322 (chain J) in PDB entry 3KC3
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 THR 315 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B MET 4.5 6.4 + - - +
308B THR* 4.3 17.9 - - + +
309B GLU* 5.9 4.9 - - + -
312B GLN* 6.2 0.7 - - - +
246J MET* 3.8 4.7 - - - -
313J ARG 4.4 5.8 - - - +
314J MET* 1.3 83.1 - - - +
316J ILE* 1.3 74.9 + - + +
317J THR* 3.5 8.1 + - - -
318J GLU* 3.3 31.0 + - - +
319J PHE* 3.0 21.7 + - - +
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Residues in contact with ILE 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B MET* 5.2 10.5 - - + -
171J GLY* 4.0 6.7 - - - +
174J ILE* 4.0 5.6 - - + -
175J GLN* 3.6 37.0 - - + +
178J HIS* 3.1 48.2 - - + +
242J LYS* 5.1 3.4 - - + -
246J MET* 3.6 22.2 - - + -
249J LEU* 5.2 0.9 - - + -
315J THR* 1.3 76.6 - - + -
317J THR* 1.3 58.3 + - - +
319J PHE* 3.0 10.8 + - + +
320J MET* 2.7 47.5 + - + +
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Residues in contact with THR 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B MET* 2.9 40.2 + - - +
282B GLY 3.6 23.6 - - - +
283B GLN* 4.3 15.9 - - + +
175J GLN* 4.6 14.1 + - - +
315J THR* 3.3 4.7 + - - -
316J ILE* 1.3 77.1 - - - +
318J GLU* 1.3 55.7 + - + +
320J MET* 3.0 2.5 + - - -
321J ASN* 2.7 53.8 + - + +
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Residues in contact with GLU 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B LYS* 3.1 39.4 + - - +
312B GLN* 4.7 3.7 - - - +
313J ARG 4.6 0.5 - - - +
314J MET* 3.1 40.0 - - + +
315J THR* 3.3 21.7 + - - +
316J ILE 3.2 0.6 - - - -
317J THR* 1.3 76.7 - - + +
319J PHE* 1.3 64.1 + - - +
321J ASN* 3.2 3.6 + - - -
322J HIS* 2.9 24.8 + - - +
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Residues in contact with PHE 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J MET* 4.0 27.8 - - + -
171J GLY* 4.3 1.6 - - - -
246J MET* 5.3 1.1 - - - -
249J LEU* 3.6 31.2 - - + -
253J MET* 3.6 22.2 - - + -
301J LEU* 3.9 16.8 - - + -
305J LEU* 3.8 20.2 - - + -
314J MET* 3.6 9.7 - - + -
315J THR 3.0 14.0 + - - +
316J ILE* 3.2 12.8 - - + +
318J GLU* 1.3 77.9 - - - +
320J MET* 1.3 95.8 + - + +
322J HIS* 3.2 15.7 - - - +
325J ILE* 3.5 35.2 - - + +
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Residues in contact with MET 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168J LYS* 4.2 11.0 - - - +
171J GLY* 3.4 18.8 - - - +
172J GLU* 4.0 20.9 - - - -
175J GLN* 3.4 34.8 - - + +
316J ILE* 2.7 22.6 + - + +
317J THR 3.6 3.4 - - - +
319J PHE* 1.3 117.9 - - + +
321J ASN* 1.3 67.5 + - - +
322J HIS 3.1 1.6 + - - -
325J ILE* 3.9 16.7 - - + +
326J MET* 3.2 25.7 + - - +
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Residues in contact with ASN 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B TYR 5.7 3.5 + - - -
285B GLU* 6.2 2.0 - - - +
175J GLN* 5.6 1.0 + - - -
317J THR* 2.7 41.2 + - + +
318J GLU* 3.6 4.3 - - - +
320J MET* 1.3 74.2 - - - +
322J HIS* 1.3 62.4 + - - +
323J PRO* 3.6 5.9 - - - +
326J MET* 3.6 28.9 - - + +
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Residues in contact with HIS 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297J GLU* 3.5 33.4 + - + +
301J LEU* 3.4 41.2 - - + +
314J MET* 4.9 7.0 - - + -
318J GLU 2.9 10.4 + - - +
319J PHE* 3.2 17.5 - - - +
320J MET 3.1 0.8 - - - -
321J ASN* 1.3 77.2 - - - +
323J PRO* 1.4 80.7 - - + +
324J TRP* 3.0 21.9 + - + +
325J ILE* 3.0 5.7 + - + -
326J MET* 2.6 33.7 + - - +
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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