Contacts of the helix formed by residues 342 - 357 (chain B) in PDB entry 3K3B
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 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.9 7.1 - - - +
29B ASN* 5.1 1.6 - - - +
32B GLU* 3.0 32.3 + - - +
106B GLN* 3.1 34.8 + - - +
337B SER* 3.7 16.1 + - - +
339B ALA 3.1 6.8 + - - -
340B SER 3.1 0.6 - - - -
341B LEU* 1.3 88.6 - - - +
343B LEU* 1.3 61.6 + - - +
344B GLU 3.5 2.4 + - - -
345B GLU* 3.6 4.7 + - - +
346B THR* 2.9 24.0 + - - -
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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
----------------------------------------------------------
231A TYR* 4.0 14.1 - - + -
234A ARG* 3.2 34.1 - - - +
40B ILE* 3.1 33.7 - - + -
52B VAL* 3.6 13.9 - - + -
53B ARG 4.5 10.1 - - - +
54B THR* 6.0 1.8 - - - -
339B ALA 3.5 1.5 + - - -
340B SER 3.0 15.6 + - - +
341B LEU 3.5 1.2 + - - -
342B ASN* 1.3 77.4 - - - +
344B GLU* 1.3 57.8 + - - +
346B THR* 3.1 5.8 + - - -
347B LEU* 2.9 57.9 + - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ARG* 3.8 22.2 + - - +
342B ASN 3.5 0.6 - - - -
343B LEU* 1.3 79.6 - - - +
345B GLU* 1.3 64.4 + - - +
347B LEU* 3.6 16.3 + - - +
348B SER* 3.1 27.7 + - - -
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 3.4 49.1 - - + +
269B SER* 4.1 1.4 + - - +
270B GLU* 3.4 41.5 + - + +
271B ASN* 5.4 0.5 - - - +
342B ASN* 3.6 4.3 + - - +
343B LEU 3.3 0.2 - - - -
344B GLU* 1.3 83.2 - - - +
346B THR* 1.3 59.9 + - - +
348B SER* 3.6 19.9 + - - -
349B THR* 3.0 32.2 + - - -
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 4.0 15.3 - - + -
52B VAL* 5.5 4.0 - - + -
106B GLN* 5.0 1.4 + - - -
336B ILE* 3.8 23.6 - - + +
337B SER* 3.3 31.3 + - - +
339B ALA 5.0 0.4 + - - -
342B ASN 2.9 19.3 + - - -
343B LEU* 3.1 12.1 + - - -
345B GLU* 1.3 75.3 - - - +
347B LEU* 1.3 60.1 + - - +
349B THR* 3.2 7.2 + - - -
350B LEU* 2.9 42.1 + - + +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.5 37.2 - - + -
54B THR* 5.3 9.2 - - + +
64B LYS* 5.4 3.6 - - + -
66B TYR* 4.4 13.0 + - + +
343B LEU* 2.9 43.7 + - + +
344B GLU* 3.9 17.5 - - - +
346B THR* 1.3 76.8 - - - +
348B SER* 1.3 53.6 + - - +
350B LEU* 3.3 4.6 + - - +
351B GLU* 2.8 43.5 + - + +
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Residues in contact with SER 348 (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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104B TYR* 5.2 3.4 + - - -
269B SER* 4.6 9.4 + - - -
271B ASN* 4.9 4.9 + - - -
344B GLU 3.1 19.1 + - - -
345B GLU* 3.6 20.1 + - - -
347B LEU* 1.3 77.6 - - - +
349B THR* 1.3 56.3 + - - +
351B GLU* 3.8 6.4 - - - +
352B TYR* 3.0 28.8 + - - +
355B ARG* 5.3 1.2 + - - -
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Residues in contact with THR 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 4.0 21.5 - - + +
105B GLY* 3.8 5.0 - - - -
106B GLN* 3.9 3.3 + - - +
269B SER* 3.4 19.5 + - - -
334B ALA* 3.9 19.5 - - + -
335B THR 3.6 20.0 + - - +
336B ILE* 3.7 13.9 - - + -
345B GLU 3.0 21.4 + - - -
346B THR* 3.2 5.4 + - - -
348B SER* 1.3 76.2 - - - +
350B LEU* 1.3 57.9 + - - +
352B TYR* 3.4 2.8 + - - +
353B ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.8 30.1 - - + -
50B VAL* 3.7 36.8 - - + -
52B VAL* 3.7 22.4 - - + -
66B TYR* 3.8 23.0 - - + -
68B PHE* 4.0 5.4 - - + -
336B ILE* 4.2 15.7 - - + -
346B THR* 2.9 32.5 + - + +
347B LEU* 3.9 4.0 - - - +
349B THR* 1.3 74.5 - - + +
351B GLU* 1.3 60.4 + - - +
353B ALA* 3.8 4.0 - - + +
354B HIS* 2.9 30.0 + - - +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 2.6 30.0 + - - +
347B LEU* 2.8 24.0 + - + +
348B SER* 3.8 6.7 - - - +
350B LEU* 1.3 74.3 - - - +
352B TYR* 1.3 58.9 + - - +
354B HIS* 3.3 11.7 + - - +
355B ARG* 2.9 39.1 + - - +
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Residues in contact with TYR 352 (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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104B TYR* 3.1 55.7 - + + +
292B LEU* 2.5 35.7 + - + -
293B LEU* 4.6 10.3 - - + -
295B LEU* 3.8 15.8 - - + +
296B GLY* 3.2 25.2 + - - -
332B ILE* 5.5 8.5 - - + -
348B SER 3.0 19.5 + - - +
349B THR 3.4 4.0 + - - +
351B GLU* 1.3 77.8 - - - +
353B ALA* 1.3 64.6 + - - +
355B ARG* 3.4 31.1 + - - +
356B ALA* 3.1 25.2 + - + +
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Residues in contact with ALA 353 (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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21B VAL* 3.9 20.0 - - + +
23B VAL* 5.1 0.2 - - + -
68B PHE* 3.7 22.9 - - + -
332B ILE* 6.4 1.8 - - + -
334B ALA* 4.0 18.4 - - + -
349B THR 2.9 17.0 + - - +
350B LEU* 3.8 3.6 - - - +
352B TYR* 1.3 81.3 - - + +
354B HIS* 1.3 63.1 + - - +
356B ALA* 3.2 8.3 + - - +
357B LYS 3.2 20.6 + - - +
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Residues in contact with HIS 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.7 32.1 - + + +
67B THR 5.0 4.4 + - - -
68B PHE* 4.0 6.5 - - + -
350B LEU 2.9 19.5 + - - +
351B GLU* 3.7 15.3 - - - +
352B TYR 3.3 0.2 - - - -
353B ALA* 1.3 76.7 - - - +
355B ARG* 1.3 61.0 + - + +
357B LYS 3.2 18.3 + - - +
358B ASN* 3.0 52.9 + - - +
359B ILE 3.9 18.6 + - - -
361B ASN* 6.1 1.6 - - - -
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Residues in contact with ARG 355 (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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293B LEU* 5.0 13.3 + - - +
296B GLY* 5.3 9.1 - - - -
297B ARG* 6.2 1.4 - - - +
300B THR* 2.8 34.5 + - + +
304B GLU* 4.9 2.4 - - - +
348B SER 5.3 0.8 + - - -
351B GLU* 2.9 17.9 + - - +
352B TYR* 3.6 46.0 + - - +
354B HIS* 1.3 77.8 - - + +
356B ALA* 1.3 61.6 + - - +
358B ASN* 4.5 6.8 + - - +
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Residues in contact with ALA 356 (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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21B VAL* 4.7 2.0 - - + -
296B GLY* 4.6 4.9 - - - +
299B ILE* 3.6 25.6 - - + -
300B THR* 3.3 28.3 + - - +
303B VAL* 3.5 12.3 - - - +
304B GLU* 5.5 0.9 - - - +
332B ILE* 4.6 10.1 - - + -
352B TYR* 3.1 21.7 + - + +
353B ALA* 3.2 13.0 + - - +
355B ARG* 1.3 80.6 - - - +
357B LYS* 1.3 58.3 + - - +
358B ASN 4.2 0.3 + - - -
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Residues in contact with LYS 357 (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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16B GLY 3.6 17.4 + - - -
17B LYS* 4.4 1.8 - - - +
19B ILE* 2.8 24.0 + - - +
20B GLN* 3.7 6.1 + - - -
21B VAL* 3.5 21.8 - - + -
67B THR 5.1 1.7 - - - +
68B PHE* 5.2 2.8 - - - -
69B ASP* 2.8 41.4 + - - +
303B VAL* 3.8 27.6 - - + -
353B ALA 3.2 7.3 + - - +
354B HIS* 3.2 12.2 + - - +
356B ALA* 1.3 78.4 - - - +
358B ASN* 1.3 62.0 + - - +
359B ILE* 3.1 30.9 + - + +
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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