Contacts of the strand formed by residues 45 - 51 (chain C) in PDB entry 2VSC
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 ARG 45 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B LYS* 6.1 0.2 - - - +
41C LYS* 3.1 6.0 - - - -
42C PHE* 3.0 44.4 + - - +
43C LYS* 3.9 11.9 - - + +
44C GLY* 1.3 79.2 - - - +
46C ASP* 1.3 66.4 + - - +
47C ILE* 3.2 10.7 + - - +
60C PRO* 3.5 23.0 - - - +
62C ASP* 3.0 39.6 + - - -
63C PHE* 3.9 14.1 - - - -
90C HIS* 5.4 1.2 + - - -
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LYS* 4.3 24.8 + - - +
39C LYS* 3.4 31.7 + - - -
40C TRP 3.5 5.8 - - - +
41C LYS* 3.4 26.6 + - - +
44C GLY 4.9 1.2 - - - +
45C ARG* 1.3 73.4 + - - +
47C ILE* 1.3 61.4 + - - +
48C TYR 3.5 0.8 + - - -
49C THR* 4.3 16.9 - - + +
60C PRO* 4.0 12.1 - - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 2.8 27.0 + - + +
41C LYS 4.2 0.7 - - - -
42C PHE* 3.9 21.8 - - + +
45C ARG* 3.6 27.1 - - - +
46C ASP* 1.3 75.7 - - - +
48C TYR* 1.3 65.3 + - + +
58C THR 4.7 0.2 - - - -
59C VAL* 3.9 4.2 - - - +
60C PRO* 3.1 22.0 - - - +
63C PHE* 3.4 54.4 - - + +
66C ALA* 4.2 2.0 - - + +
80C LEU* 3.6 31.4 - - + -
94C TYR* 4.2 5.8 - - + -
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 4.7 3.4 - - + -
39C LYS* 3.3 0.5 - - - -
40C TRP* 2.8 43.1 + + + +
46C ASP 3.5 1.2 + - - -
47C ILE* 1.3 81.9 - - + +
49C THR* 1.3 81.8 + - - +
50C PHE* 3.5 12.8 - - + +
57C SER* 2.8 38.4 + - - -
58C THR 3.5 5.8 - - - -
59C VAL* 3.5 20.2 - - + -
66C ALA* 3.5 13.9 - - + -
67C LYS* 3.6 16.9 - - + +
68C ILE* 3.4 45.4 + - + +
70C VAL* 4.9 1.2 - - - +
80C LEU* 4.0 17.3 - - + -
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Residues in contact with THR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 6.4 0.2 - - - +
37C TYR* 3.8 23.6 + - - +
38C VAL 3.2 7.9 - - - -
39C LYS* 4.1 21.3 - - + -
46C ASP* 4.3 18.2 - - + +
48C TYR* 1.3 85.7 - - - +
50C PHE* 1.3 60.6 + - - +
51C ASP* 5.2 1.2 + - - +
56C LYS 4.0 0.3 + - - +
57C SER* 3.0 7.3 - - - -
58C THR* 2.9 52.2 + - - +
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Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR* 3.5 22.0 - - - -
33C THR* 4.3 8.5 - - - -
36C VAL 4.2 4.7 - - - -
37C TYR* 3.4 10.6 - - - -
38C VAL* 2.9 36.6 + - + +
48C TYR* 3.5 19.7 - - + +
49C THR* 1.3 72.2 - - - +
51C ASP* 1.3 59.4 + - - +
52C GLY* 3.4 26.9 - - - -
55C ASN* 4.1 18.6 - - - -
56C LYS 3.6 6.3 - - - -
57C SER* 3.4 16.6 - - - -
68C ILE* 4.1 7.2 - - + -
70C VAL* 3.6 29.4 - - + -
73C LEU* 3.6 32.3 - - + -
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Residues in contact with ASP 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C TYR* 3.5 31.8 - - + +
49C THR* 4.1 2.7 + - - +
50C PHE* 1.3 71.4 - - - +
52C GLY* 1.3 59.1 + - - +
53C ALA* 3.1 24.7 + - - +
54C LEU* 3.1 31.3 + - + +
55C ASN 2.9 22.7 + - - -
56C LYS* 2.9 19.7 + - + +
101C LEU* 5.7 1.0 - - - +
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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