Contacts of the helix formed by residues 346 - 367 (chain B) in PDB entry 5LK5
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 THR 346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN* 3.8 6.3 - - - +
94B GLN* 5.2 0.2 + - - -
96B THR* 4.9 0.2 - - - +
171B LEU* 4.8 4.2 - - - +
329B ASN* 3.3 42.3 - - - +
342B PHE* 2.7 49.0 + - + +
343B GLY* 3.3 7.2 + - - -
344B ASN 3.3 0.2 - - - -
345B GLU* 1.3 81.2 - - + +
347B TRP* 1.3 74.0 + - - +
349B VAL* 3.0 5.9 + - - +
350B THR* 3.0 25.9 + - - -
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Residues in contact with TRP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 4.0 14.7 - - + +
169B THR* 3.3 35.9 + - + -
170B HIS* 4.7 0.6 + - - -
171B LEU* 3.9 34.1 - - + -
187B ASP* 3.4 53.5 + - + -
188B ASN* 4.3 3.1 - - + -
343B GLY 3.1 10.9 + - - +
344B ASN* 4.0 15.9 - - - -
346B THR* 1.3 79.4 + - - +
348B GLY* 1.3 73.1 + - - +
350B THR* 3.2 7.4 + - - -
351B LYS* 3.0 68.8 + - + +
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Residues in contact with GLY 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLY 3.0 10.9 + - - -
344B ASN* 3.4 18.8 - - - -
346B THR 3.2 0.2 - - - -
347B TRP* 1.3 94.9 - - - +
349B VAL* 1.3 59.3 + - - +
351B LYS* 4.3 13.5 - - - +
352B ALA* 5.4 1.4 + - - +
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY* 5.4 0.9 - - - -
62B LYS* 4.2 27.8 - - + +
344B ASN 3.6 11.1 + - - +
345B GLU* 3.4 23.6 - - + +
346B THR 3.0 7.7 + - - +
348B GLY* 1.3 77.9 - - - +
350B THR* 1.3 61.7 + - - +
352B ALA 4.9 1.8 + - - -
353B ALA* 5.0 6.9 + - - +
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY* 3.8 5.7 - - - +
63B ASP* 2.7 41.2 + - - +
169B THR* 4.0 16.0 - - + +
329B ASN* 5.3 2.4 + - - -
346B THR 3.0 14.8 + - - -
347B TRP* 3.5 11.4 - - - -
349B VAL* 1.3 80.6 - - - +
351B LYS* 1.3 65.5 + - - +
352B ALA 3.3 0.9 + - - -
353B ALA 3.5 2.1 + - - -
354B GLU* 3.0 48.9 + - + +
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 5.7 0.3 - - - -
169B THR* 6.0 0.7 - - - -
347B TRP* 3.0 56.9 + - + +
348B GLY* 4.3 10.5 - - - +
349B VAL 3.5 0.8 - - - -
350B THR* 1.3 81.4 - - - +
352B ALA* 1.3 70.1 + - + +
354B GLU* 3.6 7.8 - - - +
355B LYS* 3.2 24.0 + - + +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLY 5.4 0.8 + - - -
349B VAL 4.9 1.4 + - - -
350B THR 3.6 0.6 - - - -
351B LYS* 1.3 84.6 - - + +
353B ALA* 1.3 60.9 + - - +
355B LYS* 3.4 7.5 + - - +
356B GLN* 3.0 31.3 + - - +
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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
----------------------------------------------------------
57B TYR 3.9 0.4 - - - +
58B GLY* 3.7 27.8 - - - +
349B VAL 5.0 6.2 + - - +
350B THR 3.5 3.5 + - - +
351B LYS 3.5 0.2 - - - -
352B ALA* 1.3 75.8 - - - +
354B GLU* 1.3 66.2 + - - +
356B GLN* 3.3 10.9 + - - +
357B MET* 2.9 25.1 + - - +
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.8 18.8 - - + -
57B TYR* 3.6 17.4 - - - -
58B GLY* 3.5 7.9 - - - +
63B ASP* 5.6 1.0 - - - +
98B LYS* 3.5 19.2 + - - +
168B PHE* 3.5 16.8 - - + +
169B THR* 2.5 51.8 + - - +
350B THR* 3.0 28.5 + - + +
351B LYS* 3.6 7.4 - - - +
353B ALA* 1.3 77.1 - - - +
355B LYS* 1.3 61.9 + - - +
357B MET* 3.4 2.1 + - - +
358B LYS* 3.0 23.6 + - - +
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 3.7 41.0 - - + -
351B LYS 3.2 14.6 + - - +
352B ALA* 3.6 6.7 - - - +
354B GLU* 1.3 79.5 - - - +
356B GLN* 1.3 58.4 + - - +
358B LYS* 3.4 1.0 + - - +
359B ASP* 2.9 61.6 + - - +
160H ASP* 3.9 16.4 + - - -
162H ARG* 6.4 0.2 - - - +
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA* 3.0 19.7 + - - +
353B ALA* 3.3 9.7 + - - +
355B LYS* 1.3 77.4 - - - +
357B MET* 1.3 62.5 + - - +
359B ASP* 3.4 8.5 + - + +
360B LYS* 3.2 35.2 + - - +
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Residues in contact with MET 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS 3.5 11.9 - - - +
56B PHE* 4.0 7.4 - - + -
57B TYR* 3.5 57.7 - - + +
353B ALA 2.9 17.3 + - - +
354B GLU 3.9 3.4 - - - +
356B GLN* 1.3 76.5 - - - +
358B LYS* 1.3 61.9 + - - +
360B LYS* 3.4 15.0 + - - +
361B GLN* 3.1 46.1 + - + +
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Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 3.7 40.0 - - + +
100B GLU 5.5 2.0 + - - -
102B ASN* 5.5 5.5 - - - +
167B GLU* 3.0 27.9 + - - +
168B PHE* 3.7 30.3 - - + -
354B GLU 3.0 16.9 + - - +
355B LYS 3.8 0.4 - - - +
357B MET* 1.3 77.5 - - - +
359B ASP* 1.3 66.1 + - - +
361B GLN* 3.2 9.3 + - + +
362B ASP* 2.9 49.2 + - - +
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Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PHE* 4.9 3.5 - - - -
355B LYS* 2.9 55.6 + - - +
356B GLN* 3.7 8.0 - - - +
358B LYS* 1.3 75.8 - - - +
360B LYS* 1.3 57.0 + - - +
362B ASP* 3.4 12.1 + - - +
363B GLU* 3.0 36.8 + - + +
160H ASP* 4.4 14.7 - - - +
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Residues in contact with LYS 360 (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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356B GLN* 3.2 23.5 + - - +
357B MET* 3.6 19.7 - - - +
358B LYS 3.1 0.6 - - - -
359B ASP* 1.3 78.1 - - - +
361B GLN* 1.3 58.5 + - + +
363B GLU* 3.3 7.7 + - - +
364B GLU* 3.0 49.9 + - + +
44D SER* 5.1 3.4 - - - +
45D ASP* 5.5 10.2 + - + +
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 3.0 34.3 + - - +
56B PHE* 3.7 24.1 - - - +
357B MET* 3.1 34.7 + - + +
358B LYS* 3.7 10.2 + - + +
360B LYS* 1.3 77.2 - - + +
362B ASP* 1.3 60.8 + - - +
364B GLU* 3.5 7.3 + - - +
365B GLN* 3.0 28.9 + - - +
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Residues in contact with ASP 362 (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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167B GLU* 4.5 3.3 - - - +
168B PHE* 5.8 0.2 - - - -
358B LYS* 2.9 52.5 + - - +
359B ASP* 3.6 11.4 - - - +
361B GLN* 1.3 75.6 - - - +
363B GLU* 1.3 64.7 + - + +
365B GLN* 3.3 8.7 + - - +
366B ARG* 3.1 22.0 + - - +
160H ASP* 5.7 2.9 - - - +
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASP* 3.0 19.0 + - + +
360B LYS* 3.6 9.6 - - - +
362B ASP* 1.3 76.5 - - + +
364B GLU* 1.3 63.9 + - - +
366B ARG* 3.2 17.6 + - - +
367B LEU* 3.4 19.8 + - - +
44D SER* 3.3 32.8 + - - +
158H ASN* 4.7 15.9 - - - +
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Residues in contact with GLU 364 (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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360B LYS* 3.0 33.8 + - + +
361B GLN* 3.9 6.5 - - - +
362B ASP 3.4 0.2 - - - -
363B GLU* 1.3 74.4 - - - +
365B GLN* 1.3 63.3 + - - +
367B LEU* 3.1 26.0 + - - +
42D HIS 5.2 1.0 - - - +
43D LYS* 4.6 8.8 - - - +
44D SER* 3.2 31.5 + - - -
45D ASP* 4.6 9.0 - - - +
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Residues in contact with GLN 365 (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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361B GLN 3.0 14.6 + - - +
362B ASP* 3.4 13.2 - - - +
364B GLU* 1.3 77.2 - - - +
366B ARG* 1.3 62.5 + - - +
367B LEU 3.2 7.8 + - - +
116F SER* 5.2 9.9 - - - -
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Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ASP 3.1 12.7 + - - +
363B GLU* 3.2 13.6 + - - +
365B GLN* 1.3 76.6 - - - +
367B LEU* 1.3 63.6 + - + +
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Residues in contact with LEU 367 (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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363B GLU* 3.5 18.2 - - - +
364B GLU* 3.1 19.5 + - - +
365B GLN 3.5 10.0 - - - +
366B ARG* 1.3 82.2 - - + +
41D LYS* 3.5 33.9 - - + +
42D HIS 4.4 7.4 - - - +
43D LYS* 4.0 4.3 - - - +
44D SER* 3.7 36.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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