Contacts of the helix formed by residues 337 - 345 (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 HIS 337 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257J LEU 4.6 2.4 + - - -
258J CYS 3.9 2.5 - - - -
289J PRO* 3.8 31.7 + - + +
290J GLU* 3.7 47.8 + - + +
293J GLU* 6.3 1.2 - - - +
335J PRO 4.8 4.2 + - - -
336J LEU* 1.3 79.1 - - - +
338J THR* 1.3 64.9 + - - +
339J SER 3.3 2.5 - - - -
340J ARG* 3.2 29.2 + - - +
341J VAL* 2.9 29.9 + - + +
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Residues in contact with THR 338 (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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147J PHE* 6.1 0.7 - - + -
150J ILE* 4.4 4.7 - - + -
158J PHE* 3.5 25.1 - - + -
255J ILE* 3.8 12.1 - - + +
256J LEU* 3.0 30.4 + - + +
257J LEU* 3.0 21.8 + - - -
258J CYS 3.3 9.9 + - - -
259J GLY* 4.4 0.9 - - - -
336J LEU* 3.0 5.5 - - - +
337J HIS* 1.3 78.1 - - - +
339J SER* 1.3 63.8 + - - +
341J VAL* 4.1 0.7 - - - +
342J LEU* 3.2 45.5 + - + +
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Residues in contact with SER 339 (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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150J ILE* 2.9 30.6 + - - +
151J GLN* 4.2 8.1 - - - +
152J ASP* 3.6 16.0 + - - -
153J ARG* 5.1 4.6 + - - +
157J ALA* 6.5 0.2 - - - -
158J PHE* 4.7 17.5 - - - +
336J LEU 4.4 4.3 + - - -
337J HIS 3.3 0.6 - - - -
338J THR* 1.3 81.2 - - - +
340J ARG* 1.3 65.2 + - - +
342J LEU* 3.5 7.0 + - - +
343J LYS* 3.5 10.6 + - - +
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Residues in contact with ARG 340 (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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289J PRO* 5.4 4.6 - - - +
290J GLU* 5.0 4.4 + - - -
337J HIS* 3.2 35.1 + - - +
339J SER* 1.3 74.2 - - - +
341J VAL* 1.3 72.8 + - - +
342J LEU 2.4 19.1 + - - -
343J LYS* 2.5 22.6 + - + +
344J GLU* 2.7 45.5 + - + +
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Residues in contact with VAL 341 (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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258J CYS 3.3 15.5 - - - +
259J GLY* 3.4 21.6 - - - +
260J TYR* 3.5 20.6 - - + -
290J GLU* 4.2 13.0 - - + +
337J HIS* 2.9 35.7 + - + +
340J ARG* 1.3 84.1 - - - +
342J LEU* 1.3 59.2 + - - +
343J LYS 3.5 0.2 - - - -
344J GLU* 3.8 12.1 - - - +
345J ASP* 3.2 33.9 + - - +
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Residues in contact with LEU 342 (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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147J PHE* 4.0 38.1 - - + +
150J ILE* 4.9 3.4 - - + -
151J GLN* 3.7 29.2 + - + +
255J ILE* 5.0 4.0 - - + -
259J GLY* 3.4 25.1 - - - +
338J THR* 3.2 35.8 + - + +
339J SER 3.7 0.9 - - - +
340J ARG 2.4 8.7 + - - -
341J VAL* 1.3 72.5 - - - +
343J LYS* 1.3 65.9 + - - +
345J ASP* 3.2 18.6 + - + +
346J LYS* 4.0 1.2 + - - -
348J ARG* 4.4 28.7 - - - +
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Residues in contact with LYS 343 (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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151J GLN* 3.5 27.6 + - - +
152J ASP* 3.5 30.2 - - - +
153J ARG 4.9 1.4 - - - +
339J SER 3.5 6.5 + - - +
340J ARG* 2.5 17.0 + - + +
342J LEU* 1.3 74.1 - - - +
344J GLU* 1.3 53.9 + - + +
345J ASP 2.7 13.2 + - - -
346J LYS* 3.3 23.0 + - + +
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Residues in contact with GLU 344 (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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340J ARG* 2.7 55.0 + - + +
341J VAL* 3.8 10.5 - - - +
343J LYS* 1.3 76.0 - - + +
345J ASP* 1.3 69.0 + - - +
346J LYS* 3.6 2.2 + - - -
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Residues in contact with ASP 345 (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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259J GLY 4.6 3.8 - - - +
260J TYR* 4.7 7.1 - - - +
341J VAL* 3.2 31.9 - - - +
342J LEU* 3.2 11.5 + - + +
343J LYS 2.7 7.1 + - - -
344J GLU* 1.3 87.5 - - - +
346J LYS* 1.3 64.3 + - - +
347J GLU* 3.2 29.3 - - - +
348J ARG* 3.7 16.6 + - + +
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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