Contacts of the strand formed by residues 81 - 84 (chain I) in PDB entry 1TX6
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 81 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I ILE 4.1 0.3 - - - +
74I CYS* 3.2 2.9 - - - -
75I THR* 3.1 42.0 + - + +
77I SER* 5.3 0.9 + - - -
80I PRO* 1.3 75.2 - - - +
82I CYS* 1.3 62.5 + - - +
113I SER* 3.0 35.7 - - - +
114I TYR 3.3 11.7 - - - +
115I PHE* 3.5 19.7 - - + +
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Residues in contact with CYS 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I TRP* 3.4 13.7 - - + -
72I ALA* 5.0 1.1 - - + -
73I ILE 3.5 3.8 - - - +
74I CYS* 2.0 46.2 - - - -
80I PRO* 4.0 15.5 - - - -
81I THR* 1.3 76.5 - - - +
83I ARG* 1.3 61.7 + - - +
113I SER* 3.4 4.8 - - - -
114I TYR 2.8 36.0 + - - +
116I GLY 4.9 0.9 - - - -
117I PRO 4.6 2.9 - - - +
118I VAL* 4.1 4.5 - - - -
119I PRO* 3.9 26.0 - - + -
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Residues in contact with ARG 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 4.7 3.4 + - - -
97B ASN* 2.9 45.5 + - - +
99B LEU* 5.1 5.7 - - - +
66I TRP* 4.2 0.2 - - - -
72I ALA* 4.7 0.7 - - - -
73I ILE* 3.1 36.6 + - + +
82I CYS* 1.3 75.2 - - - +
84I CYS* 1.3 71.5 + - - +
85I VAL* 3.6 15.2 + - + +
110I CYS 4.7 0.9 - - - +
111I ILE* 3.7 23.3 + - - +
112I ASP 3.6 11.0 - - - +
113I SER* 3.4 28.9 + - - -
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Residues in contact with CYS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I TRP* 3.2 43.4 - - + +
68I CYS 4.4 2.5 - - - -
69I CYS* 2.0 51.8 - - + -
72I ALA* 4.6 1.3 - - + +
83I ARG* 1.3 73.8 - - - +
85I VAL* 1.3 60.1 + - - +
86I ASP* 3.3 26.2 + - - +
109I VAL* 4.1 3.8 - - - +
110I CYS* 3.1 21.8 + - - +
112I ASP 4.5 0.6 + - - -
119I PRO* 5.5 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
------------------------------------------------------------
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