Contacts of the helix formed by residues 333 - 346 (chain B) in PDB entry 1KI6
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 PRO 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B THR* 4.5 12.8 - - + -
65B THR* 4.3 4.9 - - + +
68B LEU* 3.4 23.7 - - + +
216B ARG* 5.3 11.7 - - - +
331B GLN 4.4 1.8 - - - +
332B SER* 1.3 88.3 - - - +
334B ALA* 1.3 61.3 + - - +
336B CYS* 3.8 8.4 - - + +
337B ARG* 3.0 24.3 + - - +
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Residues in contact with ALA 334 (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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68B LEU* 4.3 3.9 - - + +
332B SER* 3.2 5.9 + - - +
333B PRO* 1.3 79.3 - - - +
335B GLY* 1.3 57.7 + - - +
337B ARG* 3.4 29.9 + - - +
338B ASP* 2.9 38.2 + - - +
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Residues in contact with GLY 335 (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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331B GLN* 3.8 17.9 - - - +
332B SER* 2.7 19.4 + - - -
334B ALA* 1.3 78.4 - - - +
336B CYS* 1.3 58.3 + - - -
338B ASP* 3.1 8.1 + - - +
339B ALA* 2.8 30.7 + - - +
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Residues in contact with CYS 336 (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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65B THR* 3.3 26.0 - - + -
327B LEU* 3.8 7.4 - - + +
328B ASP 4.0 5.6 - - - -
329B TYR* 3.8 31.0 - - + -
331B GLN* 3.6 28.7 - - - +
332B SER 2.7 24.6 + - - +
333B PRO* 3.8 2.0 - - - +
335B GLY* 1.3 72.7 - - - -
337B ARG* 1.3 56.8 + - - +
339B ALA* 3.3 2.4 + - - +
340B LEU* 2.8 31.6 + - - +
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Residues in contact with ARG 337 (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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65B THR* 4.4 7.5 - - - +
68B LEU* 3.6 41.5 + - + +
69B LEU* 3.8 9.3 - - + +
72B LEU* 3.3 37.2 - - - +
333B PRO 3.0 18.2 + - - +
334B ALA* 3.4 30.5 - - - +
336B CYS* 1.3 76.2 - - - +
338B ASP* 1.3 96.8 + - - +
340B LEU* 3.2 8.3 + - - +
341B LEU* 3.1 23.5 + - - +
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Residues in contact with ASP 338 (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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334B ALA* 2.9 24.1 + - - +
335B GLY* 3.6 8.6 - - - +
337B ARG* 1.3 104.2 + - - +
339B ALA* 1.3 63.9 + - - +
341B LEU* 3.1 19.2 + - - +
342B GLN* 3.3 23.9 + - - +
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Residues in contact with ALA 339 (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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327B LEU* 3.2 25.8 - - + -
331B GLN* 3.7 14.1 - - - +
335B GLY 2.8 17.2 + - - +
336B CYS 3.5 0.2 - - - +
338B ASP* 1.3 77.3 - - - +
340B LEU* 1.3 61.1 + - - +
342B GLN* 3.3 17.0 + - - +
343B LEU* 3.3 18.4 + - - +
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Residues in contact with LEU 340 (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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52B VAL* 4.6 7.0 - - + -
54B ILE* 4.1 22.7 - - + -
65B THR* 4.5 13.0 - - - +
66B THR* 4.6 4.0 - - + -
69B LEU* 3.3 38.1 - - + -
204B VAL* 4.1 27.6 - - + -
327B LEU* 3.9 19.7 - - + +
336B CYS 2.8 18.3 + - - +
337B ARG* 3.2 6.5 + - - +
339B ALA* 1.3 77.1 - - - +
341B LEU* 1.3 61.5 + - - +
343B LEU* 3.7 4.9 + - + +
344B THR* 3.2 22.3 + - - +
347B MET* 4.7 3.6 - - + -
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Residues in contact with LEU 341 (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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69B LEU* 3.4 28.0 - - + -
72B LEU* 3.6 28.7 - - + -
337B ARG* 3.1 15.0 + - - +
338B ASP* 3.1 13.2 + - - +
340B LEU* 1.3 77.6 - - - +
342B GLN* 1.3 67.9 + - - +
344B THR* 3.2 28.1 - - + +
345B SER* 4.2 4.5 + - - -
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Residues in contact with GLN 342 (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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338B ASP* 3.3 22.4 + - - +
339B ALA* 3.3 9.9 + - - +
341B LEU* 1.3 75.4 + - - +
343B LEU* 1.3 67.4 + - + +
344B THR 3.1 1.3 - - - -
345B SER* 3.1 24.8 + - - -
346B GLY 4.6 0.3 + - - -
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Residues in contact with LEU 343 (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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204B VAL* 4.3 7.6 - - + -
325B PHE* 4.2 26.8 - - + -
326B ILE 3.5 32.3 - - - +
327B LEU* 4.1 17.0 - - + -
339B ALA* 3.3 14.1 + - + +
340B LEU* 3.9 10.8 - - + +
342B GLN* 1.3 80.1 - - + +
344B THR* 1.3 64.3 + - - +
345B SER 2.8 2.3 + - - -
346B GLY* 3.1 12.6 + - - -
347B MET* 3.6 19.7 + - + +
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Residues in contact with THR 344 (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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50B LEU* 4.4 20.7 - - + +
52B VAL* 4.7 4.0 - - - +
69B LEU* 5.4 4.9 - - - +
158B THR* 6.2 0.7 - - + -
160B ILE* 5.9 0.5 - - - +
340B LEU* 3.2 15.7 + - - +
341B LEU* 3.2 27.2 - - + +
342B GLN 3.1 0.2 - - - -
343B LEU* 1.3 79.4 - - - +
345B SER* 1.3 62.3 + - - +
347B MET* 3.3 34.8 + - - +
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Residues in contact with SER 345 (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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341B LEU 4.5 4.2 + - - -
342B GLN* 3.1 16.8 + - - -
343B LEU 2.8 3.2 + - - -
344B THR* 1.3 80.2 - - - +
346B GLY* 1.3 57.2 + - - -
347B MET 3.2 8.8 + - - +
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Residues in contact with GLY 346 (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 PHE* 3.3 24.2 - - - -
342B GLN 4.6 0.6 + - - -
343B LEU 3.1 7.3 + - - -
345B SER* 1.3 76.9 - - - +
347B MET* 1.3 58.1 + - - +
348B VAL* 4.0 4.7 + - - +
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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