Contacts of the helix formed by residues 342 - 357 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.2 4.0 - - - +
29A ASN* 5.6 0.2 - - - +
32A GLU* 2.9 34.1 + - - +
106A GLN* 2.9 38.0 + - - +
337A SER* 3.3 11.6 + - - +
339A ALA* 3.1 10.0 + - - +
340A SER 3.0 0.8 - - - -
341A LEU* 1.3 90.9 - - - +
343A LEU* 1.3 63.2 + - - +
344A GLU* 3.3 4.7 + - - -
345A GLU* 3.3 3.7 + - - +
346A THR* 3.0 27.1 + - - +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 3.7 17.7 - - + -
52A VAL* 3.5 31.4 - - + -
53A ARG 3.9 7.0 - - - +
54A THR* 4.5 23.3 - - + +
55A GLY 5.5 4.3 - - - +
339A ALA 3.8 0.2 + - - -
340A SER* 3.1 17.0 + - - +
341A LEU 3.6 0.6 - - - -
342A ASN* 1.3 75.8 - - - +
344A GLU* 1.3 71.1 + - + +
346A THR* 3.7 2.4 - - - -
347A LEU* 3.0 53.7 + - + +
234B ARG* 4.0 7.9 - - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU 4.1 5.2 - - - +
342A ASN* 4.2 1.2 - - - -
343A LEU* 1.3 89.2 + - + +
345A GLU* 1.3 64.0 + - + +
347A LEU* 3.9 5.8 - - - +
348A SER* 3.0 27.8 + - - -
234B ARG* 2.8 43.6 + - - -
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Residues in contact with GLU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLN* 3.7 35.0 - - + +
269A SER* 3.8 9.4 + - - +
270A GLU* 3.5 46.6 + - + +
342A ASN* 3.3 4.9 + - - +
344A GLU* 1.3 81.9 + - + +
346A THR* 1.3 59.9 + - - +
348A SER* 3.4 14.8 + - - -
349A THR* 2.9 33.2 + - - -
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Residues in contact with THR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE* 5.7 2.5 - - + -
41A VAL* 4.2 10.1 - - + -
52A VAL* 4.4 6.7 - - + -
106A GLN* 4.7 1.9 + - - -
336A ILE* 3.9 34.3 - - + -
337A SER* 3.5 25.7 + - - +
339A ALA 5.0 0.7 + - - -
342A ASN* 3.0 25.8 + - - +
343A LEU* 3.3 5.6 + - - -
345A GLU* 1.3 75.5 - - - +
347A LEU* 1.3 60.0 + - - +
349A THR* 3.3 3.3 + - - -
350A LEU* 2.9 39.1 + - + +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 29.8 - - + -
54A THR* 4.4 16.2 - - + +
64A LYS* 4.6 8.7 - - + -
66A TYR* 3.9 22.4 + - + +
343A LEU* 3.0 43.2 + - + +
344A GLU* 3.9 5.8 - - - +
346A THR* 1.3 71.9 - - - +
348A SER* 1.3 56.1 - - - +
350A LEU* 3.3 3.8 + - - +
351A GLU* 2.7 43.3 + - + +
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.9 3.9 + - - -
269A SER* 5.2 5.1 + - - -
344A GLU 3.0 19.2 + - - -
345A GLU* 3.4 22.5 + - - -
347A LEU* 1.3 76.5 - - - +
349A THR* 1.3 56.3 + - - +
351A GLU* 3.4 6.7 + - - +
352A TYR* 2.9 29.3 + - - +
355A ARG* 4.9 2.4 + - - -
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Residues in contact with THR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 4.0 21.9 - - + +
106A GLN* 3.9 9.2 + - - +
269A SER* 3.4 19.1 + - - -
334A ALA* 3.9 20.4 - - + -
335A THR 3.7 20.2 + - - +
336A ILE* 3.7 14.1 - - + -
345A GLU 2.9 20.4 + - - -
346A THR* 3.3 5.1 + - - -
348A SER* 1.3 75.9 - - - +
350A LEU* 1.3 57.5 + - - +
352A TYR* 3.3 3.1 + - - +
353A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.9 20.9 - - + -
50A VAL* 3.6 28.7 - - + -
52A VAL* 3.5 32.3 - - + -
66A TYR* 3.6 33.1 - - + -
68A PHE* 3.9 13.1 - - + -
336A ILE* 4.2 11.2 - - + -
346A THR* 2.9 26.5 + - + +
347A LEU* 3.8 3.4 - - - +
349A THR* 1.3 73.5 - - + +
351A GLU* 1.3 61.4 + - - +
353A ALA* 3.5 4.4 + - + +
354A HIS* 2.9 30.7 + - - +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR* 2.9 29.5 + - - +
347A LEU* 2.7 26.2 + - + +
348A SER* 3.6 6.5 - - - +
350A LEU* 1.3 71.3 - - - +
352A TYR* 1.3 53.3 + - - +
354A HIS* 3.2 13.1 + - - +
355A ARG* 2.7 48.4 + - - +
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Residues in contact with TYR 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A TYR* 3.1 57.0 - + + +
292A LEU* 2.6 33.8 + - + -
293A LEU* 4.6 7.2 - - + -
295A LEU* 3.7 17.1 - - + +
296A GLY* 3.1 27.7 + - - -
299A ILE* 6.3 0.2 - - + -
332A ILE* 5.4 11.0 - - + -
348A SER 2.9 14.1 + - - +
349A THR 3.4 8.5 - - - +
351A GLU* 1.3 75.6 - - - +
353A ALA* 1.3 67.1 + - - +
355A ARG* 3.1 33.4 + - - +
356A ALA* 2.9 26.7 + - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.7 23.1 - - + +
68A PHE* 3.5 25.0 - - + -
332A ILE* 5.7 2.7 - - + -
334A ALA* 4.0 18.6 - - + -
349A THR 2.9 15.9 + - - +
350A LEU* 3.8 2.7 - - - +
352A TYR* 1.3 82.3 - - + +
354A HIS* 1.3 61.2 + - - +
356A ALA* 3.4 7.4 + - - +
357A LYS 3.3 19.2 + - - +
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Residues in contact with HIS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR* 4.0 26.2 - + + -
67A THR 4.8 8.7 - - - -
68A PHE* 4.1 5.6 - + + -
350A LEU 2.9 18.9 + - - +
351A GLU* 3.6 13.3 + - - +
353A ALA* 1.3 73.4 - - - +
355A ARG* 1.3 66.6 + - - +
357A LYS 3.4 19.1 - - - +
358A ASN* 3.5 34.4 + - - +
359A ILE 3.2 31.5 + - - -
361A ASN* 5.6 0.8 + - - -
373A CL 4.3 17.4 - - + +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.9 21.8 + - - +
296A GLY* 5.5 6.9 - - - +
300A THR* 2.8 31.2 + - + +
304A GLU* 5.4 0.5 - - - +
348A SER 4.9 1.8 + - - -
351A GLU* 2.7 21.9 + - - +
352A TYR* 3.1 52.6 + - - +
354A HIS* 1.3 75.8 + - - +
356A ALA* 1.3 58.2 + - - +
357A LYS* 3.5 0.9 + - - -
358A ASN* 4.6 3.7 + - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.7 2.7 - - + -
296A GLY* 4.3 4.9 - - - +
299A ILE* 3.5 30.0 - - + +
300A THR* 3.2 33.4 + - - +
303A VAL* 3.7 6.6 - - - +
332A ILE* 4.4 11.9 - - + -
352A TYR* 2.9 19.5 + - + +
353A ALA* 3.5 13.0 - - - +
354A HIS 3.3 0.2 - - - -
355A ARG* 1.3 76.8 - - - +
357A LYS* 1.3 60.3 + - - +
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 3.3 26.2 - - - +
17A LYS* 4.7 0.6 - - - +
19A ILE* 2.9 29.6 + - + +
20A GLN* 4.0 2.6 - - - +
21A VAL* 3.5 21.6 - - + +
67A THR 5.4 0.3 - - - +
68A PHE* 5.6 1.7 - - - -
69A ASP* 3.0 34.9 + - - +
303A VAL* 3.7 24.5 - - + -
353A ALA 3.3 8.6 + - - +
354A HIS* 3.4 10.4 - - - +
356A ALA* 1.3 80.0 - - - +
358A ASN* 1.3 58.5 + - - +
359A ILE* 2.8 31.8 + - + +
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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