Contacts of the helix formed by residues 329 - 344 (chain B) in PDB entry 1K7E
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 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B GLY* 3.0 30.1 + - - +
260B HIS* 3.8 9.5 + - - +
298B TYR* 2.3 31.5 + - - -
299B SER* 3.8 2.3 + - - -
300B ILE* 2.6 50.8 + - + +
327B ILE 4.0 0.2 + - - -
328B THR* 1.3 69.7 - - - +
330B ASP* 1.3 58.0 + - - +
332B ALA* 2.9 4.3 + - - +
333B LEU* 2.6 42.3 + - + +
353B HIS* 4.8 1.1 + - - -
394B ARG* 5.9 0.7 - - - +
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Residues in contact with ASP 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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328B THR* 3.3 7.4 + - - +
329B ASP* 1.3 78.0 - - - +
331B GLU* 1.4 66.6 + - + +
333B LEU* 3.1 6.8 + - - +
334B GLU* 2.9 24.9 + - - +
394B ARG* 2.9 42.5 + - - +
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Residues in contact with GLU 331 (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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326B SER 4.3 0.3 - - - +
327B ILE* 3.1 22.2 - - + -
328B THR* 2.7 46.5 + - - +
330B ASP* 1.4 78.6 - - + +
332B ALA* 1.3 64.2 + - - +
334B GLU* 3.4 8.3 + - - +
335B ALA 3.1 17.0 + - - -
356B ALA* 3.6 11.0 - - + +
360B LYS* 2.7 38.3 + - - -
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Residues in contact with ALA 332 (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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300B ILE* 4.8 3.6 - - + -
327B ILE* 3.9 2.9 - - + +
328B THR 2.7 18.2 + - - +
329B ASP* 2.9 4.9 + - - +
331B GLU* 1.3 75.0 - - - +
333B LEU* 1.4 62.4 + - - +
335B ALA* 3.3 1.2 + - - +
336B PHE* 3.0 19.2 + - - +
349B LEU* 4.4 3.4 - - + +
352B SER* 3.5 27.9 - - - -
353B HIS* 3.4 43.1 - - + +
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Residues in contact with LEU 333 (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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300B ILE* 3.5 35.0 - - + -
329B ASP* 2.6 20.0 + - + +
330B ASP* 3.7 8.3 - - - +
332B ALA* 1.4 72.7 - - - +
334B GLU* 1.4 62.4 + - - +
336B PHE* 3.2 7.3 + - + +
337B LYS* 3.0 28.8 + - + +
349B LEU* 3.9 6.2 - - + +
387B VAL* 3.7 37.5 - - + -
390B ILE* 3.7 33.7 - - + -
391B LEU* 5.5 7.0 - - + -
394B ARG* 4.2 16.2 - - - +
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Residues in contact with GLU 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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330B ASP 2.9 15.6 + - - +
331B GLU* 3.8 7.7 - - - +
333B LEU* 1.4 74.3 - - - +
335B ALA* 1.4 53.8 + - - +
337B LYS* 3.1 17.0 + - - +
338B THR* 2.7 62.6 + - - +
356B ALA* 5.9 0.5 - - - +
359B LEU* 3.9 5.2 - - - +
363B ARG* 2.7 40.3 + - - -
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Residues in contact with ALA 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 GLU 3.1 4.9 + - - -
332B ALA 3.6 2.9 - - - +
334B GLU* 1.4 73.9 + - - +
336B PHE* 1.3 66.9 + - - +
338B THR* 3.2 1.7 + - - -
339B LEU* 3.0 26.0 + - - +
352B SER* 3.5 26.5 - - - +
355B LEU* 3.7 11.5 - - + +
356B ALA* 3.5 28.0 - - + +
359B LEU* 3.9 17.9 - - + -
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Residues in contact with PHE 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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332B ALA 3.0 13.2 + - - +
333B LEU* 3.2 14.4 - - - +
335B ALA* 1.3 75.1 - - - +
337B LYS* 1.3 69.5 + - + +
339B LEU* 3.3 2.9 + - - +
340B CYS* 3.0 41.3 + - - -
346B ILE* 3.4 24.7 - - + -
347B PRO* 3.0 35.7 - - + +
349B LEU* 4.1 11.2 - - + -
352B SER* 3.9 14.3 + - - +
380B GLY 4.3 4.3 - - - -
383B ASP* 4.2 13.7 - - + -
384B ILE* 4.4 8.3 - - + -
387B VAL* 3.8 40.6 - - + -
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Residues in contact with LYS 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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333B LEU* 3.0 21.2 + - + +
334B GLU* 3.5 16.3 - - - +
336B PHE* 1.3 85.5 - - + +
338B THR* 1.3 60.4 + - - +
340B CYS* 3.2 8.1 + - - +
341B ARG* 2.9 32.0 + - - +
387B VAL* 5.0 2.2 - - + -
391B LEU* 4.0 39.6 - - + +
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Residues in contact with THR 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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65B ILE* 3.6 22.9 - - + -
334B GLU* 2.7 37.2 + - - -
335B ALA* 3.6 7.9 - - - -
336B PHE 3.2 0.2 - - - -
337B LYS* 1.3 80.1 - - - +
339B LEU* 1.3 57.2 + - - +
341B ARG* 3.3 1.1 + - - -
342B HIS* 2.9 46.4 + - + +
355B LEU* 5.7 1.3 - - + -
359B LEU* 4.5 9.9 - - + -
363B ARG* 3.9 11.5 + - - +
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Residues in contact with LEU 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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62B CYS* 4.9 0.9 - - - -
65B ILE* 4.7 8.1 - - + -
73B LEU* 6.5 0.2 - - + -
75B LEU* 4.0 27.4 - - + -
335B ALA 3.0 16.9 + - - +
336B PHE 3.7 3.1 - - - +
338B THR* 1.3 73.9 - - - +
340B CYS* 1.3 70.9 + - - +
341B ARG 3.1 1.1 - - - -
342B HIS 4.5 0.2 - - - +
343B GLU* 3.0 42.0 + - + +
344B GLY 3.0 6.2 + - - -
345B ILE* 3.3 30.2 + - + +
347B PRO* 3.5 31.2 - - + -
355B LEU* 3.9 19.7 - - + +
376B LEU* 4.1 7.9 - - + -
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Residues in contact with CYS 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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336B PHE* 3.0 45.0 + - - -
337B LYS* 3.2 10.3 + - - +
339B LEU* 1.3 81.4 - - - +
341B ARG* 1.3 64.0 + - + +
344B GLY* 3.2 18.2 + - - -
345B ILE 3.4 9.0 - - - +
346B ILE* 3.9 31.2 - - + -
347B PRO* 4.3 0.2 - - - -
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Residues in contact with ARG 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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337B LYS 2.9 16.2 + - - +
338B THR* 4.1 2.9 - - - +
339B LEU 3.1 0.2 - - - -
340B CYS* 1.3 81.7 - - + +
342B HIS* 1.4 83.9 + - + +
344B GLY 4.9 0.3 + - - -
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Residues in contact with HIS 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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64B ASN* 3.1 46.5 + - + +
65B ILE* 3.9 15.0 - - + -
338B THR* 2.9 43.2 + - + +
341B ARG* 1.4 101.9 + - + +
343B GLU* 1.3 61.0 + - - +
344B GLY 3.8 0.2 - - - -
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Residues in contact with GLU 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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60B THR* 5.6 2.1 - - - +
61B LYS 4.6 2.1 - - - +
62B CYS* 3.1 40.2 - - - +
63B GLN 4.7 0.5 + - - -
64B ASN* 3.3 11.4 + - - +
65B ILE* 3.2 38.0 + - + +
339B LEU* 3.0 25.4 + - + +
342B HIS* 1.3 85.1 - - - +
344B GLY* 1.3 64.8 + - - +
345B ILE* 3.4 19.4 + - + +
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Residues in contact with GLY 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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339B LEU 3.0 3.8 + - - -
340B CYS* 3.2 17.4 + - - -
341B ARG 4.7 0.4 + - - -
342B HIS 3.8 0.8 - - - -
343B GLU* 1.3 79.0 - - - +
345B ILE* 1.3 61.0 + - - +
346B ILE* 4.2 4.6 + - - +
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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