Contacts of the helix formed by residues 63 - 77 (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 HIS 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A HIS* 4.8 2.7 - - - -
59A VAL* 3.5 31.6 - - + +
60A GLY 3.9 1.2 + - - -
61A HIS 3.2 5.2 + - - -
62A THR* 1.3 74.4 - - - +
64A GLU* 1.3 74.2 + - + +
65A LYS* 3.4 25.2 + - + +
66A VAL* 2.9 21.0 + - + -
67A VAL* 2.8 25.3 + - - +
326A VAL* 3.4 31.6 - - + +
330A GLU* 2.5 34.5 + - - -
414A VAL* 5.2 0.9 - - + -
78B ILE* 4.6 3.8 - - - +
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Residues in contact with GLU 64 (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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35A HIS* 4.8 8.2 - - + -
62A THR 3.2 5.9 + - - +
63A HIS* 1.3 82.3 + - + +
65A LYS* 1.3 67.2 + - + +
67A VAL* 3.8 7.7 - - - +
68A LYS* 2.9 31.2 + - - +
1005A CD 2.5 31.7 - - - -
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Residues in contact with LYS 65 (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* 3.2 27.7 + - + +
64A GLU* 1.3 86.9 - - + +
66A VAL* 1.3 57.0 + - - +
68A LYS* 3.7 9.9 - - + +
69A ALA* 3.1 26.2 + - - +
322A ALA* 3.6 11.8 - - + +
325A ASP* 6.0 2.9 - - + -
326A VAL* 3.9 18.2 - - + +
329A TYR* 6.3 4.0 - - - -
330A GLU* 5.0 2.9 - - - +
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Residues in contact with VAL 66 (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* 4.5 1.8 - - + -
63A HIS* 2.9 26.0 + - + +
65A LYS* 1.3 73.9 - - - +
67A VAL* 1.3 67.1 + - - +
69A ALA* 3.1 3.3 + - - +
70A ILE* 2.9 24.3 + - + +
284A SER* 3.8 17.3 - - - +
319A ALA* 3.8 28.0 - - + +
322A ALA* 4.0 8.3 - - + +
323A THR* 3.6 30.5 - - - +
326A VAL* 4.8 0.7 - - + -
78B ILE* 3.5 22.4 - - + -
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Residues in contact with VAL 67 (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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62A THR* 3.8 22.9 - - - +
63A HIS 2.8 19.9 + - - +
64A GLU* 3.8 7.2 - - - +
66A VAL* 1.3 76.3 - - - +
68A LYS* 1.3 64.0 + - - +
70A ILE* 3.2 7.4 + - - +
71A ALA* 3.0 25.7 + - + +
71B ALA 5.0 3.1 - - - +
74B ALA* 3.5 31.0 - - + +
75B GLN* 4.1 22.2 - - + +
78B ILE* 4.1 6.9 - - + +
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Residues in contact with LYS 68 (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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64A GLU 2.9 20.5 + - - +
65A LYS* 3.7 10.1 - - + +
67A VAL* 1.3 78.7 - - - +
69A ALA* 1.3 57.4 + - - +
71A ALA* 3.4 3.7 + - - +
72A ASP* 3.0 61.1 + - - +
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Residues in contact with ALA 69 (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 3.1 18.8 + - - +
66A VAL 3.1 4.9 + - - +
68A LYS* 1.3 73.3 - - - +
70A ILE* 1.3 68.0 + - - +
72A ASP* 4.2 2.9 - - - +
73A GLN* 2.9 28.6 + - - +
318A ALA* 3.7 33.4 - - + +
319A ALA 4.3 0.2 - - - +
322A ALA* 3.9 8.5 - - + -
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Residues in contact with ILE 70 (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* 2.9 18.6 + - + +
67A VAL 3.6 5.6 - - - +
69A ALA* 1.3 76.8 - - - +
71A ALA* 1.3 58.2 + - - +
73A GLN* 3.9 1.2 - - - +
74A ALA* 2.9 31.5 + - - +
286A MET* 4.2 18.8 - - + -
315A VAL* 3.8 23.0 - - + +
319A ALA* 3.7 25.6 - - + -
70B ILE* 3.6 25.8 - - + -
74B ALA* 3.9 19.1 - - + -
78B ILE* 3.8 27.8 - - + -
315B VAL* 4.7 4.9 - - + -
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Residues in contact with ALA 71 (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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67A VAL* 3.0 19.9 + - + +
68A LYS* 4.0 4.7 - - - +
70A ILE* 1.3 77.2 - - - +
72A ASP* 1.3 70.3 + - - +
74A ALA* 3.4 7.1 + - - +
75A GLN* 3.2 23.4 + - - +
67B VAL* 4.8 2.4 - - - +
71B ALA* 4.1 28.2 - - + +
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Residues in contact with ASP 72 (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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68A LYS* 3.0 51.9 + - - +
69A ALA* 4.2 3.7 - - - +
71A ALA* 1.3 80.4 - - - +
73A GLN* 1.4 63.0 + - - +
75A GLN* 3.4 13.2 + - - +
76A LYS* 3.2 22.3 - - + +
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Residues in contact with GLN 73 (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 2.9 19.6 + - - +
70A ILE 3.9 2.2 - - - +
72A ASP* 1.4 74.0 - - - +
74A ALA* 1.3 61.5 + - - +
76A LYS* 3.0 20.3 + - - +
77A LEU* 2.9 54.7 + - - +
87A HIS* 6.1 0.2 - - - +
89A PRO* 3.5 25.0 - - - +
314A PRO* 3.4 35.1 - - - +
315A VAL* 3.7 8.7 - - + +
318A ALA* 3.8 11.4 - - + +
32B ASP 5.0 2.8 + - - -
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Residues in contact with ALA 74 (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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70A ILE 2.9 18.2 + - - +
71A ALA* 3.7 6.5 - - - +
72A ASP 3.3 0.2 - - - -
73A GLN* 1.3 75.7 - - - +
75A GLN* 1.3 60.9 + - - +
77A LEU 3.9 2.0 + - - -
78A ILE* 3.6 7.1 - - + +
315A VAL* 3.9 14.5 - - + +
62B THR* 3.3 18.7 - - - +
67B VAL* 3.4 22.4 - - + +
70B ILE* 4.0 30.7 - - + -
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Residues in contact with GLN 75 (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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71A ALA 3.2 10.7 + - - +
72A ASP* 3.5 13.9 - - - +
73A GLN 3.1 0.6 - - - -
74A ALA* 1.3 80.9 - - - +
76A LYS* 1.3 61.0 + - + +
34B ALA 4.9 0.7 - - - +
62B THR* 3.7 12.2 + - - +
64B GLU* 6.1 4.2 - - - +
67B VAL* 3.8 25.9 - - - +
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Residues in contact with LYS 76 (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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72A ASP* 3.2 20.2 - - + +
73A GLN* 3.0 19.2 + - - +
75A GLN* 1.3 78.5 - - + +
77A LEU* 1.3 59.5 + - - +
32B ASP* 3.3 43.9 + - - +
33B HIS* 3.4 14.4 - - + +
34B ALA 2.9 36.0 + - - +
62B THR* 3.5 1.6 - - - -
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Residues in contact with LEU 77 (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* 2.9 36.2 + - - +
74A ALA 4.2 0.2 - - - -
76A LYS* 1.3 76.4 - - - +
78A ILE* 1.3 66.8 + - - +
79A HIS 3.3 28.0 - - - +
80A TYR* 4.1 17.3 - - + +
87A HIS* 4.3 9.4 - - + -
314A PRO* 3.6 14.5 - - + +
315A VAL* 3.8 3.5 - - - +
31B ILE* 3.9 34.3 - - + +
32B ASP 4.5 6.7 - - - +
33B HIS* 4.6 0.9 - - - -
34B ALA* 4.0 13.7 - - + -
61B HIS* 3.6 21.8 - - + +
62B THR* 3.7 3.7 - - - +
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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