Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 1SOI
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 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 4.2 0.4 + - - -
56A GLU* 1.3 75.7 - - - +
58A PRO* 1.3 72.5 - - - +
59A GLN* 2.8 38.4 + - - +
60A ASP* 3.1 28.7 + - - +
61A ALA* 3.1 20.6 + - - +
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Residues in contact with PRO 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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14A ARG* 4.9 8.1 - - - +
16A ALA* 3.2 12.1 - - - +
52A VAL* 4.0 24.0 - - + -
56A GLU 3.4 9.4 - - - +
57A ASN* 1.3 90.5 - - - +
59A GLN* 1.3 57.4 + - - +
61A ALA 3.4 0.7 + - - -
62A ALA 3.0 22.5 + - - -
96A HIS* 4.1 29.2 - - + +
98A TRP* 3.5 17.5 - - + -
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Residues in contact with GLN 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 ASN* 2.8 14.4 + - - +
58A PRO* 1.3 77.4 - - - +
60A ASP* 1.3 68.1 + - - +
62A ALA* 3.3 11.8 + - - +
63A VAL* 3.4 14.8 + - + +
76A PRO* 3.4 32.3 + - + +
98A TRP* 3.4 44.6 + - + +
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Residues in contact with ASP 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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56A GLU* 5.4 4.0 - - - +
57A ASN* 3.1 32.1 + - + +
59A GLN* 1.3 80.4 + - - +
61A ALA* 1.3 62.1 + - - +
63A VAL* 3.2 11.1 + - - +
64A ARG* 3.1 24.9 + - - +
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Residues in contact with ALA 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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16A ALA* 4.2 1.1 - - + -
51A ALA 4.5 1.6 - - - +
52A VAL* 3.8 22.4 - - + -
56A GLU* 3.5 22.6 + - - +
57A ASN 3.1 11.3 + - - +
58A PRO 3.5 9.0 - - - +
59A GLN 3.2 0.2 - - - -
60A ASP* 1.3 75.6 - - - +
62A ALA* 1.3 60.6 + - - +
64A ARG* 3.3 17.6 + - - +
65A GLU* 2.8 37.6 + - + +
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Residues in contact with ALA 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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16A ALA* 3.7 18.7 - - + +
17A GLY* 4.0 12.7 - - - +
18A VAL* 4.1 11.9 - - + +
58A PRO 3.0 14.2 + - - +
59A GLN 3.5 9.9 - - - +
60A ASP 3.2 0.2 - - - -
61A ALA* 1.3 76.6 - - - +
63A VAL* 1.3 62.4 + - + +
65A GLU* 4.3 0.2 - - - +
66A ALA* 3.1 26.5 + - - +
76A PRO* 6.1 1.3 - - + -
98A TRP* 3.8 23.6 - - + -
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Residues in contact with VAL 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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18A VAL* 6.0 0.7 - - + -
59A GLN 3.7 11.7 - - - +
60A ASP* 3.2 12.5 + - - +
61A ALA 3.2 0.2 - - - -
62A ALA* 1.3 79.0 - - + +
64A ARG* 1.3 63.3 + - - +
66A ALA* 3.5 2.3 + - - +
67A CYS* 3.2 22.6 + - + +
72A LEU 5.0 0.2 - - - +
73A ARG* 5.9 2.9 - - - -
74A VAL* 3.6 34.4 - - + +
76A PRO* 3.5 35.0 - - + -
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Residues in contact with ARG 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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51A ALA 3.5 12.9 + - - -
53A GLU* 4.2 10.1 - - - +
56A GLU* 2.8 42.6 + - - -
60A ASP* 3.1 9.2 + - - +
61A ALA* 3.7 16.2 - - - +
63A VAL* 1.3 81.0 - - - +
65A GLU* 1.3 81.0 + - - +
67A CYS* 3.1 7.9 + - - +
68A GLU* 2.9 49.0 + - + +
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Residues in contact with GLU 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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16A ALA 4.3 3.6 - - - +
49A SER 3.8 3.9 - - - +
50A GLY* 3.4 45.2 - - - +
51A ALA 3.7 14.9 + - - +
61A ALA 2.8 26.1 + - - +
62A ALA 4.3 0.2 - - - +
64A ARG* 1.3 102.1 + - - +
66A ALA* 1.3 62.6 + - - +
68A GLU* 2.9 15.6 + - - +
69A GLU* 3.2 30.2 + - - +
301A SM 2.4 29.6 - - - -
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Residues in contact with ALA 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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18A VAL* 4.1 18.6 - - + -
28A LEU* 6.3 0.7 - - + -
48A PRO* 4.0 19.7 - - + +
62A ALA 3.1 20.1 + - - +
63A VAL 3.7 4.7 - - - +
64A ARG 3.2 0.2 - - - -
65A GLU* 1.3 76.7 - - - +
67A CYS* 1.3 62.2 + - - +
69A GLU 3.4 1.0 + - - -
70A THR* 2.9 33.6 + - - +
72A LEU 4.2 0.9 - - - -
74A VAL* 4.0 22.4 - - + -
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Residues in contact with CYS 67 (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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63A VAL* 3.2 10.5 + - + +
64A ARG* 3.1 10.6 + - - +
66A ALA* 1.3 80.7 - - - +
68A GLU* 1.3 59.3 + - + +
71A GLY* 2.7 34.3 + - - -
72A LEU 3.2 20.6 + - - +
73A ARG* 3.3 49.1 - - - -
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Residues in contact with GLU 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 ARG* 2.9 39.3 + - + +
65A GLU* 2.9 22.0 + - - +
67A CYS* 1.3 78.9 - - + +
69A GLU* 1.3 60.1 + - + +
71A GLY 4.7 0.5 + - - -
111A ALA* 3.3 23.0 - - - +
301A SM 2.4 29.4 - - - -
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Residues in contact with GLU 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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30A VAL* 3.6 15.7 - - + +
46A HIS* 3.8 15.2 - - - -
48A PRO* 3.2 9.3 - - + +
49A SER 3.0 40.3 + - - +
65A GLU* 3.2 17.0 + - + +
66A ALA 4.1 2.0 - - - +
68A GLU* 1.3 82.2 - - + +
70A THR* 1.3 61.1 + - + +
71A GLY 3.7 0.2 - - - -
110A PRO* 3.5 5.7 - - - +
111A ALA* 3.2 22.4 + - - +
116A ILE* 3.7 36.7 - - + +
119A ALA* 4.5 3.5 - - - +
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Residues in contact with THR 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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28A LEU* 3.8 23.9 - - + +
30A VAL* 4.0 13.0 - - + -
48A PRO* 3.9 17.3 - - + -
66A ALA* 2.9 21.2 + - - +
69A GLU* 1.3 79.6 - - - +
71A GLY* 1.3 61.4 + - - +
72A LEU* 3.1 20.4 + - - +
74A VAL* 5.5 0.3 - - - +
108A LEU* 3.5 19.1 - - - +
109A ALA 3.2 29.2 + - - +
110A PRO* 4.2 4.0 - - - -
119A ALA* 4.1 8.7 - - + -
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Residues in contact with GLY 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 CYS* 2.7 25.8 + - - -
68A GLU 4.6 0.6 + - - -
69A GLU 3.7 0.8 - - - -
70A THR* 1.3 72.5 - - - +
72A LEU* 1.3 62.0 + - - +
73A ARG* 3.5 17.5 + - - -
106A GLN* 4.0 4.3 + - - -
107A THR 4.8 3.9 - - - +
109A ALA* 3.7 16.3 + - - +
111A ALA* 6.1 0.2 - - - +
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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