Contacts of the helix formed by residues 54 - 69 (chain A) in PDB entry 3SI5
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 THR 54 (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* 1.3 62.0 + - - +
56A SER* 3.7 8.7 - - - +
57A GLN* 3.5 45.6 + - - +
58A GLN* 3.0 27.7 + - - +
84A TRP* 4.9 0.3 - - - -
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Residues in contact with GLY 55 (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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54A THR* 1.3 73.2 - - - +
56A SER* 1.3 63.8 + - - +
57A GLN 3.3 0.2 + - - -
58A GLN* 3.3 3.1 + - - +
59A LYS* 3.0 36.2 + - - +
84A TRP* 3.9 17.2 - - - -
89A TYR* 5.2 3.8 - - - -
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Residues in contact with SER 56 (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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54A THR 3.7 6.9 - - - +
55A GLY* 1.3 75.7 - - - +
57A GLN* 1.3 58.8 + - - +
59A LYS* 3.4 12.4 + - - +
60A ARG* 3.0 43.8 + - - +
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Residues in contact with GLN 57 (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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54A THR* 3.5 34.3 + - - +
55A GLY 3.2 0.8 - - - -
56A SER* 1.3 78.5 - - - +
58A GLN* 1.3 59.7 + - - +
60A ARG* 3.4 22.2 + - - +
61A ALA* 3.0 28.2 + - - +
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Residues in contact with GLN 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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54A THR 3.0 18.9 + - - +
57A GLN* 1.3 73.4 - - - +
59A LYS* 1.3 66.4 - - - +
61A ALA* 3.2 13.8 + - - +
62A PHE* 3.0 44.8 + - + -
84A TRP* 3.2 46.0 + - + +
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Residues in contact with LYS 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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55A GLY 3.0 26.6 + - - +
56A SER* 3.8 9.2 - - - +
58A GLN* 1.3 76.4 - - - +
60A ARG* 1.3 61.9 + - - +
62A PHE* 3.2 4.9 + - - +
63A GLU* 3.0 28.1 + - + +
81A TYR* 3.9 22.5 + - + +
84A TRP* 3.7 20.9 - - + -
89A TYR* 2.7 30.3 + - + -
95A GLU* 2.9 24.2 + - - +
96A SER 5.0 2.7 + - - +
97A ASN* 4.0 15.3 + - - +
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Residues in contact with ARG 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 SER* 3.0 26.6 + - - +
57A GLN* 3.7 30.3 - - - +
59A LYS* 1.3 75.2 - - - +
61A ALA* 1.3 57.4 + - - +
63A GLU* 3.2 8.8 + - + +
64A TYR* 2.9 58.0 + - + -
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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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57A GLN 3.0 14.9 + - - +
58A GLN* 3.2 21.3 + - - +
60A ARG* 1.3 76.9 - - - +
62A PHE* 1.3 57.0 + - - +
64A TYR* 3.5 7.9 + - - +
65A GLU* 2.9 29.1 + - - +
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Residues in contact with PHE 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 GLN* 3.0 46.1 + - + -
59A LYS* 3.5 7.0 - - - +
61A ALA* 1.3 74.5 - - - +
63A GLU* 1.3 60.2 + - - +
65A GLU* 3.1 13.7 + - - +
66A ILE* 2.9 34.9 + - - +
77A VAL* 4.1 7.4 - - + +
80A ARG* 3.4 42.8 - - + -
81A TYR* 3.5 55.9 - + + -
84A TRP* 3.7 24.5 - + + -
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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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59A LYS* 3.0 21.1 + - + +
60A ARG* 3.2 11.2 + - + +
62A PHE* 1.3 77.2 - - - +
64A TYR* 1.3 63.4 + - + +
66A ILE* 3.4 14.3 + - - +
67A ARG* 3.4 11.6 + - - +
81A TYR* 2.7 27.1 + - - +
104A ARG* 2.8 44.9 + - - -
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Residues in contact with TYR 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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60A ARG* 2.9 51.7 + - + +
61A ALA* 3.8 7.4 - - - +
63A GLU* 1.3 76.7 - - + +
65A GLU* 1.3 60.3 + - - +
67A ARG* 3.1 15.2 + - + +
68A PHE* 2.8 58.9 + + + +
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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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61A ALA 2.9 19.5 + - - +
62A PHE* 3.1 13.1 + - - +
64A TYR* 1.3 72.9 - - - +
66A ILE* 1.3 65.2 + - - +
68A PHE* 4.4 2.5 - - - +
69A TYR* 2.8 43.9 + - + +
77A VAL* 3.5 21.1 - - + +
80A ARG* 2.7 45.3 + - - -
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Residues in contact with ILE 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 PHE 2.9 19.7 + - - +
63A GLU* 3.5 11.2 - - - +
65A GLU* 1.3 76.4 - - - +
67A ARG* 1.3 63.0 + - - +
69A TYR* 4.2 7.3 + - - +
77A VAL* 3.7 19.1 - - + -
78A TRP* 3.5 52.9 - - + +
81A TYR* 3.9 18.8 - - + -
104A ARG* 4.0 16.2 - - - +
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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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63A GLU 3.4 8.1 + - - +
64A TYR* 3.1 21.0 + - + +
66A ILE* 1.3 84.8 - - + +
68A PHE* 1.3 101.6 + - + +
69A TYR 3.7 1.9 + - - +
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Residues in contact with PHE 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 TYR* 2.8 51.8 + + + +
65A GLU* 5.1 1.6 - - - -
67A ARG* 1.3 123.1 - - + +
69A TYR* 1.3 68.3 + - - +
70A THR* 3.2 17.0 + - - +
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Residues in contact with TYR 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 GLU* 2.8 34.5 + - + +
66A ILE 4.3 6.7 - - - +
67A ARG 3.5 3.7 - - - +
68A PHE* 1.3 77.5 - - - +
70A THR* 1.3 59.3 + - - +
71A GLY* 3.3 34.4 - - - +
72A ASN 3.4 3.5 + - - -
73A ASP* 2.9 34.4 + - - +
74A PRO* 3.5 32.8 - - + -
76A ASP* 4.7 9.4 - - - +
77A VAL* 3.5 22.9 - - + -
80A ARG* 5.1 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