Contacts of the helix formed by residues 313 - 330 (chain A) in PDB entry 5WYF
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 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE 3.0 18.2 + - - -
79A HIS* 3.3 11.6 + - - +
287A PRO 5.4 0.2 - - - +
288A LEU* 4.6 1.8 - - - +
310A THR 3.2 15.9 + - - +
311A ALA 3.2 2.8 - - - -
312A GLY* 1.3 73.3 - - - +
314A PRO* 1.3 65.9 - - - +
315A VAL* 2.8 32.4 + - - +
316A CYS* 2.9 30.5 + - - +
317A SER* 2.7 28.6 + - - -
285B GLY 2.9 28.1 + - - -
286B MET* 3.6 10.3 - - - +
287B PRO* 4.3 2.7 - - + -
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Residues in contact with PRO 314 (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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73A GLN* 3.4 18.9 - - - +
77A LEU* 3.6 24.9 - - + +
78A ILE 3.6 4.9 - - - +
79A HIS* 3.5 23.3 - - - +
80A TYR 4.1 0.4 - - - +
87A HIS* 3.4 45.1 - - + +
89A PRO* 3.8 4.1 - - + +
313A ASN* 1.3 86.0 - - - +
315A VAL* 1.3 59.7 + - - +
317A SER* 3.6 2.0 - - - -
318A ALA* 2.8 31.7 + - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.8 37.1 - - + +
73A GLN* 3.7 6.3 - - + -
74A ALA* 3.9 26.9 - - + +
77A LEU 3.8 11.2 - - - +
78A ILE* 3.6 20.6 - - + +
286A MET* 4.5 2.5 - - + -
313A ASN* 2.8 11.9 + - - +
314A PRO* 1.3 72.2 - - - +
316A CYS* 1.3 63.6 + - - +
318A ALA* 3.8 1.9 - - - +
319A ALA* 3.0 22.0 + - - +
70B ILE* 4.9 2.9 - - + -
286B MET* 3.9 23.8 - - + -
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Residues in contact with CYS 316 (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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283A ALA* 3.5 5.2 - - - +
286A MET* 3.9 22.9 - - + -
287A PRO* 3.4 29.2 - - - +
288A LEU* 3.9 12.3 - - + +
313A ASN* 2.9 34.5 + - + +
315A VAL* 1.3 76.9 - - - +
317A SER* 1.3 56.9 + - - +
319A ALA* 3.4 5.7 + - - -
320A SER* 3.0 28.9 + - - -
286B MET* 4.2 7.2 - - - -
287B PRO* 3.9 12.8 - - - -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 3.7 3.5 - - - -
89A PRO* 3.6 29.2 - - - -
90A GLY* 3.7 6.4 - - - -
93A LEU* 3.8 16.7 - - - +
111A PHE* 4.9 0.5 - - - -
288A LEU* 4.4 1.9 - - - +
312A GLY* 3.4 17.8 + - - -
313A ASN 2.7 26.8 + - - -
314A PRO* 3.6 5.6 - - - -
316A CYS* 1.3 73.2 - - - +
318A ALA* 1.3 57.3 + - - +
320A SER* 3.1 4.0 + - - -
321A LEU* 2.9 31.9 + - - +
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Residues in contact with ALA 318 (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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69A ALA* 3.7 16.4 - - + +
73A GLN* 3.8 28.9 - - + +
89A PRO* 3.8 9.3 - - + +
314A PRO 2.8 19.9 + - - +
315A VAL 3.8 2.2 - - - +
317A SER* 1.3 72.4 - - - +
319A ALA* 1.3 61.5 + - - +
321A LEU* 3.3 10.0 + - + +
322A ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 319 (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 VAL* 3.8 17.3 - - + +
69A ALA* 4.3 7.1 - - - +
70A ILE* 3.7 24.2 - - + +
283A ALA* 4.1 13.5 - - - +
286A MET* 4.2 5.4 - - + -
315A VAL 3.0 17.2 + - - +
316A CYS 3.7 4.9 - - - +
317A SER 3.3 0.2 - - - -
318A ALA* 1.3 76.0 - - - +
320A SER* 1.3 52.3 + - - +
322A ALA* 3.5 2.6 + - - +
323A THR* 2.6 37.7 + - - -
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Residues in contact with SER 320 (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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93A LEU* 3.4 27.5 - - - +
282A LEU* 2.8 37.4 + - - +
283A ALA* 3.7 8.5 - - - +
288A LEU* 3.8 4.0 - - - -
316A CYS 3.0 17.9 + - - -
317A SER 3.1 5.1 + - - -
319A ALA* 1.3 75.1 - - - +
321A LEU* 1.3 60.1 + - - +
323A THR* 3.0 1.6 + - - -
324A LEU* 2.8 31.7 + - - +
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Residues in contact with LEU 321 (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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89A PRO* 3.7 29.8 - - + +
92A GLU* 3.9 26.0 - - + +
93A LEU* 3.8 34.8 - - + +
96A LYS* 4.3 21.2 - - + -
317A SER 2.9 17.3 + - - +
318A ALA* 3.7 8.7 - - - +
320A SER* 1.3 75.8 - - - +
322A ALA* 1.3 57.0 + - - +
324A LEU* 3.5 4.1 + - - +
325A ASP* 3.0 36.7 + - - +
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Residues in contact with ALA 322 (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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65A LYS* 3.6 30.6 - - + +
66A VAL* 4.0 10.1 - - + -
69A ALA* 3.9 8.1 - - + -
318A ALA 3.1 16.0 + - - +
319A ALA 3.7 4.9 - - - +
321A LEU* 1.3 73.1 - - - +
323A THR* 1.3 60.7 + - - +
325A ASP* 3.3 8.9 + - - +
326A VAL* 2.9 32.9 + - - +
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Residues in contact with THR 323 (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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59A VAL* 3.5 20.2 - - + +
66A VAL* 3.6 8.1 - - - +
281A SER* 3.4 22.7 - - - +
282A LEU* 3.7 7.2 - - - +
284A SER* 2.7 34.7 + - - +
319A ALA 2.6 24.8 + - - -
320A SER 3.0 4.9 + - - -
322A ALA* 1.3 75.8 - - - +
324A LEU* 1.3 63.1 + - + +
326A VAL* 3.2 4.9 + - - +
327A ILE* 3.0 29.3 + - + +
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Residues in contact with LEU 324 (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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93A LEU* 3.7 29.8 - - + -
96A LYS* 3.8 28.0 - - + +
97A LEU* 4.1 13.5 - - + -
100A ILE* 4.1 16.6 - - + -
256A LEU* 3.7 30.5 - - + -
262A MET* 4.5 5.9 - - + +
282A LEU* 4.6 11.2 - - + +
320A SER* 2.8 21.1 + - - +
321A LEU* 4.0 3.8 - - - +
323A THR* 1.3 76.2 - - + +
325A ASP* 1.3 62.0 + - - +
327A ILE* 3.4 11.4 + - + +
328A GLU* 3.2 21.7 + - - +
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Residues in contact with ASP 325 (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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65A LYS* 6.0 3.4 - - + -
96A LYS* 4.1 18.3 + - - -
321A LEU* 3.0 24.3 + - - +
322A ALA* 3.5 8.2 - - - +
323A THR 3.2 0.2 - - - -
324A LEU* 1.3 73.4 - - - +
326A VAL* 1.3 67.8 + - + +
328A GLU* 3.3 4.6 + - - +
329A TYR* 3.0 59.4 + - + -
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Residues in contact with VAL 326 (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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59A VAL* 3.8 18.2 - - + -
63A HIS* 3.4 51.4 - - + +
65A LYS* 3.9 17.7 - - + -
66A VAL* 4.8 2.0 - - + -
322A ALA 2.9 20.0 + - - +
323A THR* 3.2 8.3 + - - +
325A ASP* 1.3 75.0 - - - +
327A ILE* 1.3 58.5 + - - +
329A TYR* 5.1 1.8 - - - -
330A GLU* 2.7 48.3 + - - +
332A LEU* 4.0 7.0 - - + -
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Residues in contact with ILE 327 (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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58A ASN* 5.0 5.8 - - + -
59A VAL* 3.6 18.8 - - + -
256A LEU* 3.7 43.1 - - + +
257A GLY* 5.5 0.2 - - - -
262A MET* 4.4 13.2 - - + -
281A SER 5.7 0.4 - - - +
323A THR* 3.0 25.7 + - + +
324A LEU* 3.6 14.6 - - + +
325A ASP 3.3 0.2 - - - -
326A VAL* 1.3 77.4 - - - +
328A GLU* 1.3 61.8 + - - +
331A GLY* 3.2 1.9 + - - -
332A LEU* 2.8 45.1 + - + -
333A VAL* 4.0 26.5 + - + +
413A LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 328 (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 LYS* 5.5 6.8 + - - -
324A LEU 3.2 11.2 + - - +
325A ASP* 3.8 8.3 - - - +
326A VAL 3.2 0.6 - - - -
327A ILE* 1.3 79.9 - - - +
329A TYR* 1.3 95.4 + - + +
331A GLY* 3.0 19.5 + - - -
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Residues in contact with TYR 329 (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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65A LYS* 6.3 4.0 - - - -
325A ASP* 3.0 50.4 + - + +
326A VAL* 4.6 1.8 - - - +
328A GLU* 1.3 103.5 + - + +
330A GLU* 1.3 63.5 + - + +
331A GLY 3.3 0.7 - - - -
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Residues in contact with GLU 330 (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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63A HIS* 2.5 39.1 + - - -
65A LYS* 5.0 3.8 - - - +
326A VAL* 2.7 32.7 + - + +
329A TYR* 1.3 76.0 - - + +
331A GLY* 1.3 65.0 + - - +
332A LEU* 3.3 17.4 + - + +
335A LYS* 5.2 3.1 - - - +
414A VAL* 4.0 16.1 - - - +
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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
------------------------------------------------------------
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