Contacts of the helix formed by residues 333 - 352 (chain A) in PDB entry 5UAK
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 LEU 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 6.0 0.4 - - - +
332A ILE* 1.3 76.3 - - - +
334A ARG* 1.3 63.7 + - - +
335A LYS 3.5 0.7 - - - -
336A ILE* 3.2 14.4 - - + +
337A PHE* 3.1 42.2 - - + -
914A TYR* 4.2 37.0 - - + +
917A TYR* 4.3 28.5 - - + +
1126A GLU* 3.7 35.2 - - + +
1127A GLY* 5.2 4.0 - - - +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 4.0 24.8 + - - +
106A ILE* 3.5 31.5 - - + +
107A ALA* 4.4 19.8 - - - +
110A ASP* 5.1 6.5 + - - +
332A ILE* 3.9 18.5 - - + +
333A LEU* 1.3 80.5 - - - +
335A LYS* 1.3 73.6 + - - +
337A PHE* 3.4 19.6 + - - +
338A THR* 3.8 7.8 + - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 3.8 34.7 - - - +
218A LEU* 3.7 36.9 - - + +
325A TYR* 5.5 4.0 - - + +
332A ILE* 3.6 33.6 - - + +
333A LEU 3.5 0.2 - - - -
334A ARG* 1.3 88.2 - - - +
336A ILE* 1.3 63.7 + - + +
338A THR* 3.3 27.1 - - + +
339A THR* 3.3 19.6 + - + +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.4 25.9 - - + +
325A TYR* 6.2 2.0 - - + -
332A ILE* 3.3 25.8 - - + +
333A LEU* 3.2 23.8 - - + +
335A LYS* 1.3 75.7 - - - +
337A PHE* 1.3 84.2 + - + +
339A THR* 2.7 19.5 + - - -
340A ILE* 3.5 15.1 - - + +
914A TYR 4.9 8.3 - - - +
915A VAL* 6.2 2.5 - - + -
917A TYR* 4.7 14.6 - - + -
918A ILE* 5.1 17.8 - - + +
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 5.4 1.8 - - + -
106A ILE* 4.7 19.5 - - + -
333A LEU* 3.1 43.7 - - + -
334A ARG* 3.4 11.4 + - - +
335A LYS 3.3 0.6 - - - -
336A ILE* 1.3 89.4 - - + +
338A THR* 1.3 59.9 + - - +
340A ILE* 3.0 32.6 + - + +
341A SER* 3.7 3.1 + - - -
917A TYR* 4.6 20.2 - + + -
921A GLY* 6.3 2.7 - - - -
1126A GLU 5.4 1.6 - - - -
1127A GLY* 4.6 12.6 - - - -
1130A GLY* 4.6 7.0 - - - -
1131A ILE* 4.2 31.2 - - + -
1134A THR* 3.9 33.8 - - + +
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Residues in contact with THR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 3.1 24.9 + - - +
100A LEU* 5.2 0.2 - - - -
102A LEU* 4.6 7.8 - - - +
103A GLY* 5.1 10.3 - - - -
334A ARG* 3.8 9.1 + - - +
335A LYS* 3.3 29.8 - - + +
337A PHE* 1.3 79.6 - - - +
339A THR* 1.3 60.8 - - + +
341A SER* 2.7 22.5 + - - -
342A PHE* 3.0 38.9 + - + -
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 4.7 17.8 - - + +
218A LEU* 6.5 0.9 - - + -
318A VAL* 4.6 8.6 - - - +
322A VAL* 4.5 13.5 - - + +
335A LYS* 3.3 20.8 + - + +
336A ILE* 2.7 30.6 + - - -
338A THR* 1.3 78.0 - - + +
340A ILE* 1.3 54.4 + - - +
342A PHE* 3.4 10.8 + - + +
343A CYS* 2.8 37.0 + - - +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 3.7 14.8 - - + -
336A ILE* 3.5 11.4 - - + +
337A PHE* 3.0 19.2 + - + +
339A THR* 1.3 76.1 - - - +
341A SER* 1.3 59.7 + - - +
343A CYS* 3.1 4.0 + - - -
344A ILE* 3.0 48.5 + - + +
918A ILE* 3.6 39.5 - - + -
921A GLY 5.6 2.9 - - - +
922A VAL* 3.7 23.6 - - + +
1134A THR* 5.7 8.5 - - + +
1138A ASN* 4.8 2.7 - - - +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 6.3 0.4 - - - -
99A PRO* 3.2 32.9 - - - +
102A LEU* 3.7 12.7 - - - +
337A PHE 3.7 1.8 + - - -
338A THR* 2.7 27.0 + - - -
340A ILE* 1.3 78.3 - - - +
342A PHE* 1.3 58.7 + - - +
345A VAL* 3.3 23.7 + - - +
1134A THR* 5.9 4.5 - - - -
1137A MET* 5.7 7.6 - - - -
1138A ASN* 3.8 18.6 + - - +
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Residues in contact with PHE 342 (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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96A ALA* 3.5 20.6 - - - -
99A PRO* 3.7 15.9 - - + -
100A LEU* 3.8 20.4 - - + -
211A LEU* 3.7 15.4 - - + +
214A LEU* 3.7 48.2 - - + -
215A ILE* 4.2 18.2 - - + -
216A TRP* 6.2 1.8 - + - -
338A THR* 3.0 49.0 + - + -
339A THR* 3.7 12.1 - - + +
341A SER* 1.3 76.3 - - - +
343A CYS* 1.3 62.5 + - - +
345A VAL* 3.5 7.7 + - - +
346A LEU* 3.3 16.8 + - - +
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Residues in contact with CYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 5.7 6.1 - - + -
226A GLY* 6.5 0.2 - - - -
317A VAL* 3.7 44.9 - - - -
318A VAL* 3.7 19.5 - - + -
321A SER* 5.5 1.6 - - - -
339A THR 2.8 21.7 + - - +
340A ILE 3.1 1.3 + - - +
342A PHE* 1.3 71.2 - - - +
344A ILE* 1.3 61.0 + - - +
346A LEU* 3.1 16.5 + - - +
347A ARG* 2.8 27.6 + - - +
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLY* 4.8 15.7 - - - +
317A VAL* 5.6 1.1 - - + -
318A VAL* 4.8 8.5 - - + -
340A ILE* 3.0 34.0 + - + +
343A CYS* 1.3 80.7 - - + +
345A VAL* 1.3 57.3 + - + +
347A ARG* 3.4 30.8 + - - +
348A MET* 2.9 34.8 + - + +
922A VAL* 5.1 7.9 - - + -
924A ASP* 5.9 4.7 - - + +
1138A ASN* 3.2 42.4 - - - +
1141A SER* 5.6 0.9 - - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS* 4.4 31.9 - - + +
96A ALA* 4.7 4.0 - - - +
207A GLN* 3.7 27.6 - - + +
211A LEU* 4.2 11.7 - - + -
341A SER 3.3 18.6 + - - +
342A PHE* 3.5 8.9 + - - +
343A CYS 3.2 0.6 - - - -
344A ILE* 1.3 75.7 - - + +
346A LEU* 1.3 64.5 + - - +
348A MET* 3.4 8.0 + - + +
349A ALA* 3.2 22.0 + - - +
1138A ASN* 4.9 9.0 - - - +
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Residues in contact with LEU 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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208A VAL* 3.5 35.9 - - + -
211A LEU* 3.7 26.0 - - + +
226A GLY 5.6 0.4 - - - -
227A LEU* 4.0 28.7 - - + +
230A LEU* 3.9 19.3 - - + -
317A VAL* 5.4 1.8 - - + -
342A PHE 3.3 8.2 + - - +
343A CYS* 3.1 20.5 + - - +
345A VAL* 1.3 76.7 - - - +
347A ARG* 1.3 64.1 + - - +
349A ALA* 3.3 3.8 + - + +
350A VAL* 3.1 30.7 + - + +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.7 24.2 - - + -
310A PHE* 2.8 61.9 + - - -
313A SER* 4.4 12.6 - - - +
314A GLY* 4.6 11.5 - - - +
317A VAL* 5.3 6.5 - - + -
343A CYS 2.8 19.0 + - - +
344A ILE* 3.6 25.7 + - - +
345A VAL 3.3 0.2 - - - -
346A LEU* 1.3 71.7 - - - +
348A MET* 1.3 78.9 + - - +
351A THR* 2.9 44.8 + - + +
352A ARG 4.0 0.3 + - - -
924A ASP* 2.7 33.5 + - - -
1145A TRP* 4.9 3.2 - - - -
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Residues in contact with MET 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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310A PHE* 4.6 11.0 - - - -
344A ILE* 2.9 23.4 + - + +
345A VAL* 3.5 10.1 - - + +
346A LEU 3.4 0.2 - - - -
347A ARG* 1.3 88.2 - - - +
349A ALA* 1.3 58.2 + - - +
352A ARG* 3.8 7.5 + - - +
353A GLN* 3.1 41.5 + - + +
1138A ASN* 5.7 0.4 - - - +
1141A SER* 3.7 26.0 - - - +
1145A TRP* 3.6 40.2 - - + -
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Residues in contact with ALA 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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204A ALA* 4.6 17.7 - - + +
207A GLN* 4.4 21.5 - - + -
208A VAL* 5.7 1.3 - - + +
211A LEU* 5.4 1.1 - - + -
345A VAL 3.2 10.9 + - - +
346A LEU* 3.7 10.8 - - + +
347A ARG 3.2 0.2 - - - -
348A MET* 1.3 81.0 - - - +
350A VAL* 1.3 60.1 + - + +
353A GLN* 3.6 12.9 + - - +
354A PHE* 2.9 34.6 + - - +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 6.0 0.4 - - - -
208A VAL* 6.1 2.0 - - + -
227A LEU* 4.2 19.7 - - + -
230A LEU* 3.4 32.1 - - + +
231A ILE* 4.6 15.0 - - + -
234A ALA* 4.9 9.2 - - + +
346A LEU* 3.1 27.4 + - + +
349A ALA* 1.3 80.4 - - + +
351A THR* 1.3 65.7 + - - +
354A PHE* 4.3 11.4 - - + +
355A PRO* 3.5 16.5 - - - +
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.4 27.7 - - + +
233A LEU* 4.1 12.3 - - + -
234A ALA* 5.1 11.6 - - - +
237A GLN* 3.6 35.1 - - - +
310A PHE* 3.8 26.0 - - + -
313A SER* 6.3 0.4 - - - -
347A ARG* 2.9 20.5 + - + +
350A VAL* 1.3 77.4 - - - +
352A ARG* 1.3 59.1 + - - +
355A PRO* 3.4 17.1 - - - +
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Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 3.6 41.2 - - + -
311A PHE* 5.5 5.3 - - - -
348A MET* 3.8 12.0 + - - +
351A THR* 1.3 79.0 - - - +
353A GLN* 1.3 63.5 + - - +
354A PHE 3.6 0.9 - - - -
355A PRO* 3.8 6.4 - - - +
356A TRP* 3.4 59.0 + - + -
993A ASP* 5.0 11.3 + - - -
1145A TRP* 3.3 51.8 - - - -
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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