Contacts of the helix formed by residues 66 - 80 (chain A) in PDB entry 6P7B
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLN* 4.1 6.7 + - - +
63A GLY* 3.1 21.5 + - - -
64A PHE 3.3 3.0 + - - +
65A LYS* 1.3 78.6 - - - +
67A PRO* 1.3 69.6 - - - +
68A ASN* 3.9 14.3 + - - +
69A SER* 2.7 35.0 + - - -
70A LYS* 5.4 0.3 - - - +
17E C 5.0 5.0 + - - -
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.7 24.9 - - + -
66A SER* 1.3 82.9 - - - +
68A ASN* 1.3 68.2 + - - +
69A SER 3.1 2.5 - - - -
70A LYS* 3.1 33.8 + - + +
71A ILE* 3.1 21.8 + - - +
17E C 3.3 37.2 - - - +
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Residues in contact with ASN 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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8A ILE* 3.4 27.3 + - + +
9A GLY* 3.8 19.8 - - - -
10A ILE* 4.4 9.9 + - - +
62A GLN* 3.6 38.4 + - + +
66A SER* 3.1 8.9 - - - +
67A PRO* 1.3 81.9 - - - +
69A SER* 1.3 58.0 + - - +
71A ILE* 3.6 9.9 - - - +
72A ILE* 2.8 34.0 + - - +
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Residues in contact with SER 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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62A GLN* 4.4 2.2 - - - +
63A GLY 3.4 23.1 - - - -
64A PHE* 3.6 19.9 + - - -
66A SER* 2.7 22.5 + - - -
68A ASN* 1.3 75.7 - - - +
70A LYS* 1.3 61.6 + - - +
72A ILE* 3.1 12.2 + - - +
73A TYR* 2.9 50.7 + - - -
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Residues in contact with LYS 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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10A ILE* 4.6 8.3 - - - +
41A TRP* 3.7 26.4 - - + +
66A SER 5.4 0.2 - - - +
67A PRO* 3.1 38.9 + - + +
69A SER* 1.3 82.7 + - - +
71A ILE* 1.3 63.0 + - + +
73A TYR* 3.9 4.7 - - - +
74A PHE* 2.9 29.8 + - - +
70C LYS* 6.2 0.2 - - - +
73C TYR* 3.6 43.8 - - + +
16E T 3.4 27.8 - - - -
17E C 3.2 25.1 + - - +
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Residues in contact with ILE 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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8A ILE* 3.7 29.6 - - + -
10A ILE* 4.6 25.1 - - + +
37A TRP* 3.9 28.0 - - + -
41A TRP* 3.8 26.9 - - + -
45A VAL* 4.0 11.2 - - + -
67A PRO 3.1 14.3 + - - +
68A ASN* 3.6 10.3 - - - +
70A LYS* 1.3 83.2 - - + +
72A ILE* 1.3 62.1 + - - +
74A PHE* 3.3 1.6 + - - +
75A ILE* 2.9 41.8 + - + +
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Residues in contact with ILE 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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8A ILE* 4.7 12.1 - - + -
59A LEU* 4.8 12.6 - - + +
60A GLU 3.7 13.0 - - - +
61A LYS* 4.6 3.1 - - - -
62A GLN* 3.5 41.1 - - + +
68A ASN 2.8 17.1 + - - +
69A SER* 3.1 11.4 + - - +
71A ILE* 1.3 76.4 - - - +
73A TYR* 1.3 66.2 + - + +
75A ILE* 3.2 9.7 + - - +
76A LYS* 2.9 49.3 + - + +
88A VAL* 4.7 11.9 - - + -
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Residues in contact with TYR 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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64A PHE* 4.8 12.3 - + - -
69A SER* 2.9 43.6 + - - +
70A LYS* 4.1 4.7 - - - +
72A ILE* 1.3 78.6 - - + +
74A PHE* 1.3 65.6 + - - +
76A LYS* 3.5 24.4 - - + +
77A GLY 3.0 18.9 + - - -
41C TRP* 3.7 26.5 - + - -
70C LYS* 3.4 63.5 + - + +
73C TYR* 4.3 7.6 - - + -
74C PHE* 3.6 10.3 - - + +
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Residues in contact with PHE 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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41A TRP* 3.6 21.1 - + + -
42A GLU* 3.5 59.5 - - + -
45A VAL* 4.1 21.8 - - + -
46A ALA* 4.8 2.0 - - + -
70A LYS 2.9 19.3 + - - +
71A ILE 3.6 1.8 - - - +
73A TYR* 1.3 76.0 - - - +
75A ILE* 1.3 58.2 + - + +
77A GLY 3.3 1.0 + - - -
78A PHE* 2.9 39.0 + + + +
73C TYR* 3.6 14.9 + + + +
76C LYS* 4.1 3.1 - - + -
77C GLY* 3.6 30.4 - - - -
80C TYR* 3.8 26.2 - + + -
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Residues in contact with ILE 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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6A VAL* 5.7 1.1 - - + -
8A ILE* 5.4 4.9 - - + -
37A TRP* 5.0 5.8 - - + -
45A VAL* 3.7 21.8 - - + -
49A LEU* 3.6 21.8 - - + -
57A VAL* 4.6 2.0 - - + -
59A LEU* 4.3 27.1 - - + -
71A ILE* 2.9 39.4 + - + +
72A ILE* 3.6 5.2 - - - +
74A PHE* 1.3 72.0 - - + +
76A LYS* 1.3 66.7 + - - +
78A PHE* 3.6 6.4 - - + +
79A PHE* 3.0 37.4 + - + +
86A VAL* 3.8 21.5 - - + +
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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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59A LEU* 5.8 2.5 - - + -
72A ILE* 2.9 24.2 + - + +
73A TYR* 3.5 33.2 - - + +
74A PHE 3.3 0.2 - - - -
75A ILE* 1.3 76.0 - - - +
77A GLY* 1.3 62.6 + - - +
79A PHE 4.0 0.3 - - - -
80A TYR* 3.0 28.4 + - - +
86A VAL* 4.2 28.2 + - + +
88A VAL* 4.2 24.7 - - + +
42C GLU* 3.1 33.5 + - - +
74C PHE* 4.0 10.7 - - + -
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Residues in contact with GLY 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 TYR 3.0 11.9 + - - -
74A PHE 3.8 2.0 - - - -
76A LYS* 1.3 77.1 - - - +
78A PHE* 1.3 64.2 + - - +
80A TYR* 3.3 12.4 + - - +
81A ASN* 4.5 0.7 + - - +
74C PHE* 3.5 38.0 - - - -
77C GLY 3.4 7.2 - - - -
78C PHE* 3.2 17.5 - - - +
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Residues in contact with PHE 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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45A VAL* 5.9 1.6 - - + -
46A ALA* 3.9 21.8 - - + -
49A LEU* 5.5 2.2 - - + -
50A THR* 3.6 33.0 - - + -
74A PHE* 2.9 30.7 + + + +
75A ILE* 3.1 7.6 + - - +
77A GLY* 1.3 77.6 - - - +
79A PHE* 1.3 88.5 + + - +
80A TYR 3.4 0.5 + - - -
81A ASN* 4.0 5.9 + - - +
77C GLY* 3.1 21.9 - - - +
80C TYR* 3.9 28.5 - + + -
81C ASN* 3.5 41.5 + - - +
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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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49A LEU* 3.8 44.2 - - + -
50A THR* 4.2 8.7 - - + -
54A PRO* 4.9 3.8 - - + -
57A VAL* 3.9 19.1 - - + -
75A ILE* 3.0 15.4 + - + -
76A LYS 4.0 0.4 - - - -
78A PHE* 1.3 104.0 - + - +
80A TYR* 1.3 56.9 + - - +
81A ASN* 2.9 11.9 + - - -
82A SER* 3.8 4.6 + - - -
84A THR* 3.0 59.2 + - + +
86A VAL* 3.9 33.4 - - + -
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Residues in contact with TYR 80 (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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76A LYS 3.0 21.0 + - - +
77A GLY* 3.6 11.4 - - - +
78A PHE 3.3 2.4 - - - -
79A PHE* 1.3 75.2 - - - +
81A ASN* 1.3 60.1 + - - +
85A LYS* 6.3 1.6 - - - -
86A VAL* 5.8 5.6 - - + -
40C ASN* 4.6 1.8 + - - -
42C GLU* 3.9 27.6 - - + -
43C ARG* 3.2 39.6 + - - +
46C ALA* 3.7 21.1 - - + -
74C PHE* 4.1 9.6 - + + -
78C PHE* 4.0 21.6 - + + -
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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