Contacts of the strand formed by residues 46 - 50 (chain A) in PDB entry 1T5A
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 GLY 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 4.0 2.9 - - - -
44A ASN 3.6 4.8 + - - -
45A THR* 1.3 75.0 - - - +
47A ILE* 1.3 58.9 + - - -
48A ILE* 5.2 0.2 - - - -
70A ASN* 4.2 9.0 - - - -
71A VAL* 6.4 0.4 - - - -
357A ASP 2.9 11.7 + - - -
358A CYS* 3.3 19.3 - - - +
359A ILE* 3.1 27.5 + - - +
464A HIS* 4.1 11.7 + - - -
467A ARG* 5.5 0.2 - - - +
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Residues in contact with ILE 47 (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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43A ARG* 3.4 32.5 - - - +
45A THR 4.0 2.2 - - - +
46A GLY* 1.3 75.7 - - - +
48A ILE* 1.3 66.2 + - - +
49A CYS* 3.8 22.8 + - - -
68A GLY 4.1 4.3 - - - +
69A MET* 3.9 3.9 - - - -
70A ASN* 2.9 40.3 + - - +
71A VAL 3.3 3.6 + - - -
359A ILE* 3.7 15.0 - - + -
361A LEU* 4.8 1.3 - - + -
375A VAL* 4.0 12.8 - - + +
378A GLN* 3.5 25.8 - - + +
379A ASN* 3.6 26.5 - - + +
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Residues in contact with ILE 48 (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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47A ILE* 1.3 75.8 - - - +
49A CYS* 1.3 62.9 + - - +
71A VAL* 3.5 36.3 - - + +
73A ARG* 4.0 24.7 - - + -
241A PHE* 4.1 12.6 - - + -
325A ILE* 3.5 45.1 - - + -
358A CYS* 3.9 18.4 - - + -
359A ILE 3.1 8.4 + - - +
360A MET* 3.3 18.8 - - + +
361A LEU* 3.1 26.0 + - - +
465A LEU* 5.0 2.7 - - + -
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Residues in contact with CYS 49 (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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47A ILE* 3.8 15.7 - - - -
48A ILE* 1.3 71.5 - - - +
50A THR* 1.3 62.1 + - - +
51A ILE* 3.3 7.3 + - + +
64A MET* 4.8 2.5 - - - -
69A MET* 3.6 35.4 - - - -
71A VAL 2.9 9.3 + - - -
72A ALA* 3.4 5.4 - - - -
73A ARG* 2.8 24.5 + - - -
361A LEU* 4.0 5.4 - - - -
365A THR* 3.7 13.0 - - - +
375A VAL* 3.3 33.2 - - - -
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Residues in contact with THR 50 (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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48A ILE 4.2 0.2 - - - -
49A CYS* 1.3 69.7 - - - +
51A ILE* 1.3 70.0 + - - +
55A SER* 3.9 0.2 + - - -
73A ARG* 2.8 57.0 + - - +
75A ASN* 4.3 13.9 - - + +
360A MET* 4.5 1.0 - - - +
361A LEU 2.9 22.5 + - - -
362A SER* 3.4 12.8 + - - -
365A THR* 3.0 18.2 + - - +
366A ALA* 3.4 21.9 + - + -
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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