Contacts of the strand formed by residues 50 - 55 (chain C) in PDB entry 1T0R
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 ILE 50 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PRO 4.8 3.6 - - - +
48C GLU 4.5 6.5 - - - +
49C LYS* 1.3 85.9 - - - +
51C LEU* 1.3 77.8 + - - +
52C ARG* 3.6 15.6 + - + +
64C ARG* 3.8 40.2 - - - +
82C ILE 3.5 1.6 - - - +
83C PHE* 3.7 1.1 - - - -
84C MET* 2.7 40.7 + - - +
85C ASP* 4.5 11.9 - - - +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.9 14.1 - - + -
27C MET 5.3 1.4 - - - +
28C ASP* 4.9 9.5 - - - +
31C ALA* 3.9 30.3 - - + +
32C GLU* 4.6 11.2 - - - +
35C ALA* 3.9 27.8 - - + -
39C ILE* 5.2 2.7 - - + -
49C LYS 5.9 0.2 - - - +
50C ILE* 1.3 77.1 - - - +
52C ARG* 1.3 67.8 + - - +
81C ILE* 4.4 5.8 - - + -
82C ILE 3.3 6.5 - - - +
83C PHE* 3.3 43.3 - - + -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ILE* 3.9 12.3 - - + +
51C LEU* 1.3 83.1 - - - +
53C VAL* 1.3 65.0 + - - +
61C LEU* 3.7 31.6 - - + +
62C PHE 2.9 31.3 + - - -
63C PRO* 3.7 9.7 - - - +
64C ARG* 3.2 31.5 - - - +
81C ILE* 3.4 8.1 - - - +
82C ILE* 2.8 32.7 + - + +
84C MET* 3.2 40.0 - - + +
85C ASP 5.2 9.2 - - - +
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Residues in contact with VAL 53 (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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27C MET* 3.2 56.9 - - + +
30C VAL* 4.4 7.9 - - + -
31C ALA* 3.9 17.3 - - + +
52C ARG* 1.3 84.4 - - - +
54C ARG* 1.3 63.1 + - - +
61C LEU* 3.6 3.2 - - - +
62C PHE* 2.9 37.6 + - + +
79C LEU* 4.2 23.8 - - + -
80C ASP 3.5 9.0 - - - +
81C ILE* 4.7 4.7 - - + -
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Residues in contact with ARG 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TRP* 4.6 9.3 - - - -
53C VAL* 1.3 76.2 - - - +
55C ARG* 1.3 61.1 + - - +
59C GLY* 3.9 24.5 + - - +
60C THR 2.9 20.4 - - - +
61C LEU* 3.9 10.8 - - + -
62C PHE* 4.3 0.9 - - - -
79C LEU* 3.6 4.6 - - - -
80C ASP* 2.7 70.9 + - + +
82C ILE* 3.9 36.6 - - + +
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Residues in contact with ARG 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 1.3 69.8 - - - +
56C HIS* 1.3 60.8 + - - +
57C GLU* 4.0 14.4 - - - +
58C ASP* 3.2 39.1 + - - +
59C GLY* 3.0 29.8 + - - -
60C THR* 2.9 21.0 + - - +
62C PHE* 3.7 25.1 - - + -
71C ALA 3.1 26.7 + - - -
72C GLY 3.5 13.1 + - - -
73C LEU* 3.8 9.9 - - - +
74C ARG* 5.6 0.4 - - - +
77C GLU* 3.7 29.3 + - + +
78C THR 4.4 0.9 - - - +
79C LEU* 3.6 10.8 - - + -
80C ASP* 4.3 0.6 - - - +
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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