Contacts of the helix formed by residues 57 - 77 (chain A) in PDB entry 2W27
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 PRO 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY 3.6 7.4 - - - +
56A ILE* 1.3 100.1 - - + +
58A GLU* 1.3 68.6 + - + +
59A GLU* 3.3 8.0 + - + +
60A TYR* 3.3 36.9 + - + -
61A LYS* 3.5 7.6 + - - +
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Residues in contact with GLU 58 (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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56A ILE 4.4 3.6 - - - +
57A PRO* 1.3 73.9 - - + +
59A GLU* 1.3 66.0 + - - +
61A LYS* 3.3 9.0 + - + +
62A LEU* 3.0 29.8 + - + +
92A ASN 6.0 0.2 - - - -
93A LEU* 3.3 29.3 - - + +
96A LEU* 3.4 35.7 - - + +
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Residues in contact with GLU 59 (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 PRO* 3.2 5.6 - - + +
58A GLU* 1.3 79.4 - - - +
60A TYR* 1.3 96.8 + - + +
62A LEU* 3.3 10.3 + - - +
63A GLU* 2.8 36.7 + - - +
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Residues in contact with TYR 60 (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 LEU* 3.6 33.4 - - + -
50A PHE* 3.7 3.4 - - + -
56A ILE* 4.3 7.4 - - + -
57A PRO* 3.3 38.0 + - + +
58A GLU 3.2 0.4 - - - -
59A GLU* 1.3 109.4 + - + +
61A LYS* 1.3 63.4 + - - +
63A GLU* 3.6 23.8 - - - +
64A VAL* 3.2 29.8 + - - +
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Residues in contact with LYS 61 (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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50A PHE* 3.6 28.5 - - + +
51A PHE* 3.0 40.3 + - + +
52A LEU 4.3 1.0 - - - -
53A ASP 2.7 32.0 + - - -
54A ALA* 4.4 4.2 - - - +
56A ILE* 3.9 21.1 + - + +
57A PRO 3.5 8.0 + - - +
58A GLU* 3.3 12.4 + - + +
60A TYR* 1.3 78.2 - - - +
62A LEU* 1.3 57.0 + - - +
64A VAL 3.4 0.9 + - - -
65A ASP* 2.8 31.6 + - - +
90A ASP* 5.9 1.6 + - - -
93A LEU* 4.3 26.1 - - + +
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Residues in contact with LEU 62 (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 GLU* 3.0 25.6 + - + +
59A GLU* 3.6 9.4 - - - +
61A LYS* 1.3 73.5 - - - +
63A GLU* 1.3 59.8 + - - +
65A ASP* 3.7 16.0 - - - +
66A ASN* 3.0 30.5 + - - +
89A GLN* 5.8 2.9 - - - +
93A LEU* 4.5 31.2 - - + +
96A LEU* 4.9 11.9 - - + -
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Residues in contact with GLU 63 (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 LEU* 4.3 10.8 - - + +
11A ILE* 3.6 29.7 - - + +
59A GLU* 2.8 24.1 + - - +
60A TYR* 3.6 33.3 - - - +
62A LEU* 1.3 74.4 - - - +
64A VAL* 1.3 61.3 + - + +
66A ASN* 3.6 6.4 - - - +
67A ARG* 3.6 14.4 + - - +
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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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7A ILE* 4.6 8.3 - - + -
8A LEU* 3.7 17.5 - - + -
11A ILE* 4.4 11.2 - - + -
14A VAL* 4.3 13.9 - - + -
47A LEU* 3.9 28.7 - - + -
50A PHE* 3.6 21.5 - - + -
51A PHE* 4.1 4.7 - - + -
60A TYR 3.2 18.9 + - - +
61A LYS 3.9 2.2 - - - +
62A LEU 3.3 0.2 - - - -
63A GLU* 1.3 71.7 - - - +
65A ASP* 1.3 69.7 + - - +
66A ASN 3.0 1.6 - - - -
67A ARG* 2.8 19.9 + - + +
68A ILE* 3.2 14.5 + - + +
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Residues in contact with ASP 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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51A PHE* 4.0 11.3 - - + -
61A LYS 2.8 20.4 + - - +
62A LEU* 3.7 21.1 - - + +
64A VAL* 1.3 76.7 - - - +
66A ASN* 1.3 61.7 + - - +
68A ILE* 3.2 5.0 + - - +
69A ILE* 3.0 38.4 + - - +
89A GLN* 3.2 22.5 + - - -
93A LEU* 6.1 0.3 - - - +
502A 5GP 3.0 36.7 + - - -
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Residues in contact with ASN 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 LEU 3.0 17.8 + - - +
63A GLU* 3.6 8.5 - - - +
64A VAL 3.0 1.0 - - - -
65A ASP* 1.3 73.2 - - - +
67A ARG* 1.3 65.3 - - - +
68A ILE 3.1 0.2 + - - -
69A ILE* 3.3 5.9 + - - +
70A ARG* 2.9 55.1 + - - +
105A LEU* 3.6 24.8 - - - +
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Residues in contact with ARG 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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11A ILE* 3.5 55.1 + - + +
12A ASP* 2.8 30.2 + - - +
14A VAL* 4.5 10.3 - - + +
63A GLU* 3.6 10.1 + - - +
64A VAL* 2.8 17.1 + - - +
66A ASN* 1.3 75.4 - - - +
68A ILE* 1.3 60.8 + - - +
70A ARG* 4.2 4.8 - - - +
71A GLN* 3.2 53.2 + - - +
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Residues in contact with ILE 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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14A VAL* 3.3 22.0 - - + -
15A LEU 4.6 4.9 - - - +
16A PRO* 3.9 15.3 - - + +
34A VAL* 3.8 19.3 - - + -
35A LEU 4.4 1.1 - - - +
36A GLY* 3.8 13.2 - - - -
47A LEU* 3.6 30.5 - - + -
51A PHE* 4.0 18.2 - - + -
64A VAL* 3.2 8.2 + - + +
65A ASP* 3.6 5.6 - - - +
66A ASN 3.1 1.0 - - - -
67A ARG* 1.3 76.1 - - - +
69A ILE* 1.3 57.4 + - + +
71A GLN* 3.2 6.6 + - - +
72A ALA* 2.7 33.4 + - - +
502A 5GP 3.6 19.1 - - + +
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Residues in contact with ILE 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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34A VAL* 5.5 3.4 - - + -
65A ASP* 3.0 39.9 + - - +
66A ASN* 3.8 4.7 - - - +
68A ILE* 1.3 76.1 - - + +
70A ARG* 1.3 56.5 + - - +
72A ALA* 4.2 5.8 - - - -
73A LEU* 2.7 56.6 + - + +
87A MET* 4.6 18.2 - - + -
89A GLN* 4.0 7.6 - - - +
102A PHE* 3.9 27.4 - - + -
105A LEU* 3.9 26.7 - - + -
106A LEU* 5.9 0.4 - - + -
502A 5GP 5.9 0.9 - - - +
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Residues in contact with ARG 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 ASN* 2.9 46.1 + - - +
67A ARG* 4.2 5.6 - - - +
69A ILE* 1.3 75.8 - - + +
71A GLN* 1.3 59.2 + - + +
74A ASP* 2.8 41.0 + - - +
105A LEU* 3.1 34.7 - - + +
108A GLU* 2.9 34.8 + - - -
109A TYR* 3.6 16.5 + - - +
112A LYS* 5.2 2.2 - - - +
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Residues in contact with GLN 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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12A ASP 5.3 3.4 + - - -
14A VAL 3.1 27.7 + - - +
15A LEU* 3.4 4.0 - - - +
16A PRO* 3.3 25.2 - - + +
18A TYR* 4.1 0.5 + - - -
67A ARG* 3.2 41.9 + - - +
68A ILE 3.2 4.6 + - - +
70A ARG* 1.3 77.6 - - + +
72A ALA* 1.3 64.1 + - - +
74A ASP* 3.4 8.9 + - - +
75A ARG* 3.1 22.0 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PRO* 3.8 3.0 - - + +
18A TYR* 3.5 18.2 - - + -
34A VAL* 3.9 36.3 - - + -
68A ILE 2.7 20.6 + - - +
69A ILE* 3.5 6.3 - - - +
71A GLN* 1.3 72.5 - - - +
73A LEU* 1.3 63.9 + - + +
75A ARG* 3.0 19.4 + - - +
76A PHE* 3.0 17.8 + - + -
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Residues in contact with LEU 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 ILE* 2.7 38.7 + - + +
72A ALA* 1.3 77.7 - - + +
74A ASP* 1.3 64.7 + - - +
76A PHE* 3.3 9.0 + - + +
77A LEU* 3.1 26.9 + - - +
85A ILE* 3.7 31.9 - - + -
87A MET* 4.6 7.0 - - + -
105A LEU* 5.5 1.3 - - + +
106A LEU* 4.5 9.0 - - + -
109A TYR* 3.4 36.6 - - + -
114A ILE* 3.9 3.2 - - + +
119A PHE* 3.5 30.7 - - + -
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Residues in contact with ASP 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 ARG* 2.8 24.9 + - - +
71A GLN* 3.5 9.0 - - - +
73A LEU* 1.3 76.6 - - - +
75A ARG* 1.3 62.0 + - - +
77A LEU* 3.5 23.6 + - - +
78A GLU* 4.0 9.5 - - - +
109A TYR* 2.9 29.5 + - - -
112A LYS* 5.8 0.7 + - - -
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Residues in contact with ARG 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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18A TYR* 3.3 24.8 + - + +
71A GLN 3.1 8.4 + - - +
72A ALA 3.0 14.0 + - - +
74A ASP* 1.3 78.4 - - - +
76A PHE* 1.3 60.3 + - - +
78A GLU* 3.1 21.7 + - - +
79A ALA* 3.3 15.0 + - - +
238A GLU 4.8 3.6 + - - -
239A THR* 3.7 16.0 - - - +
240A PHE* 3.4 60.9 + - + +
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Residues in contact with PHE 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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18A TYR* 4.2 6.3 - + - -
32A TYR* 4.2 21.8 - + + -
34A VAL* 4.2 13.9 - - + -
72A ALA 3.0 29.5 + - - -
73A LEU* 3.3 3.5 + - + +
75A ARG* 1.3 71.1 - - - +
77A LEU* 1.3 64.9 + - - +
78A GLU 3.0 3.7 + - - -
79A ALA* 3.1 18.9 + - + +
80A ASP 4.5 0.3 - - - +
81A SER* 5.9 0.2 - - - -
83A LEU* 4.2 12.3 - - + -
84A LEU 4.1 10.8 - - - -
85A ILE* 3.6 46.7 - - + -
114A ILE* 3.7 21.8 - - + -
118A ARG* 4.1 22.3 + - - +
240A PHE* 3.4 34.8 - + - -
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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 LEU 3.1 18.1 + - - +
74A ASP* 3.5 17.0 - - - +
75A ARG 3.2 0.4 - - - -
76A PHE* 1.3 77.0 - - - +
78A GLU* 1.3 63.3 + - + +
79A ALA 3.6 3.0 - - - +
109A TYR* 4.3 13.9 - - + +
112A LYS* 3.1 53.4 - - + +
113A GLY* 3.8 4.9 - - - +
114A ILE* 3.7 23.1 - - + -
118A ARG* 5.9 0.4 - - - +
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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