Contacts of the helix formed by residues 63 - 79 (chain A) in PDB entry 5WWT
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 SER 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A VAL* 4.0 1.3 - - - -
59A THR* 5.2 4.9 - - - +
62A ALA* 1.3 75.9 - - - +
64A VAL* 1.3 63.5 + - - +
65A GLN 3.8 1.5 + - - -
66A HIS 3.4 9.9 + - - -
67A VAL* 3.1 23.7 + - - +
231B ASN* 2.7 20.5 + - - -
232B PRO 4.7 6.5 - - - -
233B GLN* 2.7 33.1 + - - -
234B PRO* 4.8 2.1 - - - +
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Residues in contact with VAL 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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57A VAL* 3.9 17.5 - - + -
59A THR* 4.4 10.3 - - + +
63A SER* 1.3 73.2 - - - +
65A GLN* 1.3 57.7 + - - +
67A VAL* 3.9 1.2 - - - +
68A LYS* 2.9 29.0 + - + +
88A GLN* 3.8 27.6 - - + +
93A GLN 3.5 19.5 - - - +
94A ASP* 4.0 15.0 - - - -
96A LEU* 3.7 29.2 - - + +
93B GLN* 5.2 6.5 - - - +
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Residues in contact with GLN 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 SER* 3.2 0.6 - - - -
64A VAL* 1.3 77.9 - - - +
66A HIS* 1.3 65.4 + - - +
68A LYS* 3.1 9.9 + - - +
69A ASN* 3.0 39.1 + - - +
88A GLN* 6.0 0.4 - - - -
228B HIS 3.8 3.3 - - - +
229B VAL 4.9 4.4 + - - -
231B ASN* 3.5 38.6 - - - +
398B PRO 5.6 1.2 + - - -
399B GLN* 5.0 0.6 - - - +
400B GLU* 3.3 60.9 + - + +
462B LYS* 5.1 9.1 - - - +
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Residues in contact with HIS 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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62A ALA* 4.2 12.6 - - + -
63A SER* 3.4 18.9 + - - +
65A GLN* 1.3 78.4 - - - +
67A VAL* 1.3 56.7 + - - +
69A ASN* 3.1 10.3 + - - +
70A LEU* 2.9 65.4 + - + +
215A TYR* 4.5 10.0 + + - -
231B ASN* 3.9 5.5 + - - +
233B GLN* 3.4 33.1 - - + +
319B ARG* 6.0 1.6 + - - -
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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
----------------------------------------------------------
57A VAL* 3.7 29.2 - - + -
62A ALA* 3.7 23.1 - - + -
63A SER 3.1 16.0 + - - +
64A VAL 4.0 2.9 - - - +
66A HIS* 1.3 78.1 - - - +
68A LYS* 1.3 57.4 + - - +
70A LEU* 3.4 8.6 + - - +
71A LEU* 2.9 29.3 + - + +
96A LEU* 4.0 5.6 - - + -
212A LEU* 4.6 3.1 - - + -
215A TYR* 3.7 17.9 - - + -
216A LEU* 3.5 31.4 - - + -
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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 VAL* 2.9 21.2 + - + +
65A GLN* 3.1 8.5 + - - +
67A VAL* 1.3 78.0 - - - +
69A ASN* 1.3 58.6 + - - +
71A LEU* 3.4 4.9 + - - +
72A LEU* 2.9 47.0 + - + +
86A ILE* 3.5 41.0 + - + +
88A GLN* 5.6 8.9 + - + +
96A LEU* 3.9 20.4 - - + -
400B GLU* 3.6 33.6 + - - +
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Residues in contact with ASN 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 GLN* 3.0 35.5 + - - +
66A HIS* 3.1 10.8 + - - +
68A LYS* 1.3 76.7 - - - +
70A LEU* 1.3 67.0 + - + +
72A LEU* 3.0 24.7 + - - +
73A ASP* 3.0 27.8 + - - +
400B GLU* 4.3 13.4 + - - +
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Residues in contact with LEU 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 HIS* 2.9 56.0 + - + +
67A VAL* 3.7 5.2 - - - +
69A ASN* 1.3 77.8 - - + +
71A LEU* 1.3 57.7 + - - +
73A ASP* 3.3 16.2 + - + +
74A GLU* 2.9 27.1 + - - +
212A LEU* 3.8 33.8 - - + +
215A TYR* 4.2 14.4 - - + -
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Residues in contact with LEU 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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55A VAL* 4.1 12.3 - - + -
67A VAL 2.9 17.2 + - - +
68A LYS 3.7 4.9 - - - +
70A LEU* 1.3 72.8 - - - +
72A LEU* 1.3 61.2 + - - +
74A GLU* 3.6 6.9 - - + +
75A LEU* 2.9 38.9 + - + +
86A ILE* 3.8 11.9 - - + -
96A LEU* 3.9 23.8 - - + -
98A ILE* 4.8 8.5 - - + -
208A PHE* 4.2 14.8 - - + -
211A VAL* 4.2 10.3 - - + -
212A LEU* 3.9 9.4 - - + -
216A LEU* 3.7 44.0 - - + -
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Residues in contact with LEU 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* 2.9 33.8 + - + +
69A ASN* 3.0 31.4 + - - +
71A LEU* 1.3 77.7 - - - +
73A ASP* 1.3 59.3 + - - +
75A LEU* 3.8 4.4 - - + +
76A GLN* 2.9 29.5 + - - +
84A VAL 4.8 9.4 - - - +
85A PRO* 5.6 0.4 - - + -
86A ILE* 3.7 28.2 - - + +
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Residues in contact with ASP 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 ASN* 3.0 17.2 + - - +
70A LEU* 3.5 18.7 - - + +
72A LEU* 1.3 79.2 - - - +
74A GLU* 1.3 55.6 + - - +
76A GLN* 3.1 9.8 + - - +
77A LYS* 2.9 46.3 + - - +
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Residues in contact with GLU 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 LEU 2.9 16.7 + - - +
71A LEU* 3.6 13.5 - - + +
72A LEU 3.3 0.2 - - - -
73A ASP* 1.3 75.9 - - - +
75A LEU* 1.3 61.3 + - + +
77A LYS* 3.1 26.1 + - - +
78A GLN* 2.9 62.2 + - - +
211A VAL* 3.7 32.9 - - + +
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Residues in contact with LEU 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 LEU* 2.9 28.4 + - + +
72A LEU* 3.9 6.1 - - + +
74A GLU* 1.3 80.8 - - + +
76A GLN* 1.3 65.4 + - - +
78A GLN* 4.5 6.3 - - - +
79A PHE* 3.0 38.0 + - + +
82A LEU 5.3 1.8 + - - +
84A VAL* 3.6 30.1 - - + +
86A ILE* 4.0 12.8 - - + -
98A ILE* 3.7 31.6 - - + -
206A PRO* 3.6 32.3 - - + -
208A PHE* 5.5 0.9 - - + -
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Residues in contact with GLN 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 LEU 2.9 14.9 + - - +
73A ASP* 3.1 14.8 + - - +
75A LEU* 1.3 77.0 - - - +
77A LYS* 1.3 63.4 + - + +
80A ASN* 3.5 1.7 + - - -
81A GLY* 3.1 48.6 + - - +
82A LEU 4.0 14.0 - - - +
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Residues in contact with LYS 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 ASP* 2.9 32.6 + - - +
74A GLU* 3.1 28.1 + - - +
76A GLN* 1.3 76.7 - - + +
78A GLN* 1.3 66.9 + - + +
80A ASN* 3.4 16.1 + - - +
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Residues in contact with GLN 78 (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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74A GLU* 2.9 53.3 + - - +
75A LEU* 4.3 4.5 - - + +
77A LYS* 1.3 75.9 - - + +
79A PHE* 1.3 72.0 + - + +
80A ASN* 3.2 12.0 + - - -
206A PRO* 3.5 14.6 - - - +
207A SER* 2.9 50.8 + - - +
211A VAL* 4.9 1.8 - - - +
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Residues in contact with PHE 79 (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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75A LEU* 3.0 23.8 + - + +
78A GLN* 1.3 84.7 - - + +
80A ASN* 1.3 69.0 + - - +
81A GLY 3.1 3.3 + - - -
82A LEU* 3.2 38.3 + - + +
84A VAL* 3.7 36.3 - - + -
98A ILE* 5.5 0.9 - - + -
99A PRO 6.1 0.7 - - - -
101A ILE* 5.9 0.4 - - + -
204A LEU* 3.6 40.6 - - + -
205A SER* 3.9 5.4 - - - -
206A PRO* 3.6 44.6 - - + -
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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