Contacts of the helix formed by residues 70 - 78 (chain B) in PDB entry 1S0V
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 ALA 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 4.5 5.8 + - + +
65B ALA* 4.5 11.4 - - - -
67B ASN 2.8 9.0 + - - +
69B ALA* 1.3 76.5 - - - +
71B LYS* 1.3 68.0 + - - +
72B PRO* 3.1 1.3 - - - -
73B LEU* 3.2 9.4 + - + +
74B ILE* 3.1 38.7 + - + +
123B LEU* 4.9 7.0 - - + -
254B ILE* 4.0 27.4 - - + -
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA 3.3 15.9 - - - -
66B ASP* 3.1 37.8 + - - +
67B ASN* 3.3 16.5 + - - +
68B ALA* 3.1 17.5 + - - +
70B ALA* 1.3 77.3 - - - +
72B PRO* 1.3 70.9 - - + +
73B LEU 3.0 1.2 + - - -
74B ILE* 3.1 12.9 + - - +
75B THR* 3.2 18.2 + - - +
116B TYR* 5.4 1.3 - - - -
752B LEU* 5.3 2.8 - - - +
754B GLN* 5.7 6.0 - - - +
755B PHE* 4.2 33.3 - - + -
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA 3.1 9.6 - - - +
69B ALA 2.8 19.1 - - - +
70B ALA* 3.1 0.7 - - - -
71B LYS* 1.3 94.9 - - + +
73B LEU* 1.3 68.9 + - + +
75B THR* 3.4 13.3 + - - +
76B THR* 3.3 14.6 + - - +
253B ALA 5.8 0.2 - - - +
257B ARG* 3.8 31.9 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA* 3.5 13.9 - - + +
71B LYS 3.0 1.0 + - - -
72B PRO* 1.3 81.0 - - + +
74B ILE* 1.3 67.0 + - + +
76B THR* 2.7 14.8 + - - +
77B LEU* 2.7 65.7 + - + +
123B LEU* 5.5 5.6 - - + -
226B MET* 5.4 4.0 - - + -
250B TYR* 3.8 48.7 - - + +
253B ALA* 5.1 8.7 - - + -
254B ILE* 4.9 12.8 - - + -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ALA* 3.8 38.8 - - + +
70B ALA* 3.1 25.2 + - + +
71B LYS* 3.8 4.7 - - - +
73B LEU* 1.3 91.3 - - + +
75B THR* 1.3 57.0 + - - +
77B LEU* 3.6 3.6 - - - -
78B LEU* 3.0 33.8 + - + +
116B TYR* 4.2 15.9 - - + +
119B ILE* 4.4 21.5 - - + -
120B LYS* 5.8 0.2 - - - -
123B LEU* 5.0 6.3 - - + -
755B PHE* 3.6 26.5 - - + -
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 3.2 16.4 + - - +
72B PRO* 3.8 9.5 - - - +
73B LEU 2.9 1.4 + - - -
74B ILE* 1.3 77.0 - - - +
76B THR* 1.3 62.7 + - + +
78B LEU* 5.1 0.7 - - - -
79B PRO* 3.3 19.3 - - - +
755B PHE* 3.6 24.8 - - + +
756B ARG 4.3 24.3 - - - +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO 3.3 11.4 + - - +
73B LEU* 2.7 20.4 + - - +
75B THR* 1.3 82.1 - - + +
77B LEU* 1.3 62.8 + - - +
78B LEU 3.4 1.1 - - - -
79B PRO* 3.7 13.6 - - - +
80B LYS* 4.0 12.1 - - - +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 2.7 38.7 + - + +
74B ILE* 3.9 4.9 - - + -
76B THR* 1.3 79.9 - - - +
78B LEU* 1.3 61.6 + - - +
80B LYS* 3.9 5.8 - - - +
81B MET* 3.8 13.9 + - - +
119B ILE* 3.6 23.1 - - + +
220B LEU* 4.9 4.1 - - + +
224B THR* 3.0 46.7 + - + +
226B MET* 3.4 36.8 - - + -
250B TYR* 4.3 10.3 - - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.0 16.9 + - + +
75B THR* 5.0 0.9 - - - +
77B LEU* 1.3 74.1 - - - +
79B PRO* 1.3 61.6 - - + +
80B LYS 2.9 4.3 - - - -
81B MET* 2.5 28.9 + - - +
82B ILE* 3.0 22.0 + - + +
112B GLU* 4.9 3.1 - - + +
115B ALA* 3.6 13.0 - - + -
116B TYR* 3.2 62.4 - - + +
119B ILE* 4.1 9.2 - - + -
746B ARG* 4.6 13.7 - - - -
755B PHE* 4.3 17.5 - - + +
756B ARG* 6.0 3.8 - - - -
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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