Contacts of the helix formed by residues 81 - 90 (chain A) in PDB entry 1VLP
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.2 9.4 - - + -
25A THR* 3.7 26.2 - - + +
79A TYR 3.2 6.7 - - - +
80A LEU* 1.3 86.6 - - + +
82A SER* 1.3 66.2 + - - +
83A ALA* 4.3 8.1 - - + +
84A TYR* 3.1 18.8 + - + +
85A ILE* 3.2 11.8 + - - +
259A THR* 4.0 20.6 - - + +
260A PHE* 3.9 15.5 - - + -
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Residues in contact with SER 82 (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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80A LEU 3.5 2.6 + - - -
81A PRO* 1.3 71.9 - - - +
83A ALA* 1.3 57.4 + - - +
85A ILE* 3.3 9.6 + - - +
86A LYS* 3.0 27.5 + - - +
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Residues in contact with ALA 83 (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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24A PHE* 3.5 16.5 - - + -
25A THR* 6.2 0.2 - - - +
81A PRO* 3.2 5.8 + - + +
82A SER* 1.3 76.4 - - - +
84A TYR* 1.3 60.3 + - - +
86A LYS* 3.6 8.7 + - - +
87A TYR* 3.1 27.7 + - - +
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Residues in contact with TYR 84 (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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17A ILE* 3.7 29.4 - - + +
20A HIS* 2.8 50.8 + + - +
21A ALA* 3.5 38.8 - - + -
24A PHE* 3.6 19.2 - + + -
25A THR* 4.9 0.2 - - - +
80A LEU* 4.2 13.7 - - + -
81A PRO* 3.1 18.3 + - + +
83A ALA* 1.3 75.8 - - - +
85A ILE* 1.3 69.8 + - + +
87A TYR* 3.0 13.3 + + - +
88A ILE* 2.9 56.5 + - + +
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Residues in contact with ILE 85 (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 ILE* 4.0 16.8 - - + -
73A LEU* 4.5 8.5 - - + -
74A LYS* 4.1 32.1 - - + +
80A LEU* 3.8 36.8 - - + +
81A PRO 3.2 13.6 + - - +
82A SER* 3.6 9.9 - - - +
84A TYR* 1.3 81.0 - - + +
86A LYS* 1.3 53.4 + - - +
88A ILE* 3.5 15.6 + - + +
89A SER* 2.5 46.3 + - - +
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Residues in contact with LYS 86 (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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82A SER 3.0 14.4 + - - +
83A ALA* 3.7 12.1 - - - +
85A ILE* 1.3 75.6 - - - +
87A TYR* 1.3 57.2 + - - +
89A SER* 3.3 6.1 + - - -
90A SER* 3.0 30.6 + - - -
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Residues in contact with TYR 87 (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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20A HIS* 3.0 38.3 + + - -
24A PHE* 3.5 44.6 - + + -
83A ALA 3.1 14.9 + - - +
84A TYR* 3.0 18.3 + + - +
86A LYS* 1.3 77.8 - - - +
88A ILE* 1.3 68.5 + - + +
89A SER 3.5 0.2 + - - -
90A SER* 3.6 11.1 + - - -
93A TYR* 3.4 37.2 + + - +
126A LYS* 3.4 30.6 + - + +
127A ASP* 4.6 3.6 + - - -
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Residues in contact with ILE 88 (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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20A HIS* 3.8 11.9 - - + -
65A PHE* 3.6 43.3 + - + +
70A ILE* 3.5 22.4 - - + -
73A LEU* 3.8 18.6 - - + -
84A TYR* 2.9 56.0 + - + +
85A ILE* 3.6 14.1 - - + +
87A TYR* 1.3 92.7 - - + +
89A SER* 1.3 61.4 + - - +
90A SER 3.3 1.1 - - - +
93A TYR* 3.9 19.4 - - + +
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Residues in contact with SER 89 (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 PHE* 5.7 1.9 - - - +
70A ILE* 3.7 30.2 - - - +
85A ILE* 2.5 27.6 + - - +
86A LYS* 3.6 8.5 - - - -
87A TYR 3.3 0.2 - - - -
88A ILE* 1.3 74.9 - - - +
90A SER* 1.3 65.9 + - - +
91A SER* 3.7 0.7 + - - -
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Residues in contact with SER 90 (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* 6.0 0.3 - - - -
86A LYS* 3.0 17.2 + - - -
87A TYR* 3.6 11.4 - - - -
88A ILE 3.3 2.0 - - - +
89A SER* 1.3 81.5 - - - +
91A SER* 1.3 65.2 + - - +
92A ASN* 3.0 31.0 + - - +
93A TYR* 3.1 20.7 + - - +
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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