Contacts of the strand formed by residues 32 - 36 (chain C) in PDB entry 1TT5
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 HIS 32 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER 4.9 1.8 - - - +
31C ALA* 1.3 74.9 - - - +
33C VAL* 1.3 59.1 + - - +
56C SER* 2.8 33.9 + - - +
57C PHE* 3.3 22.2 - - - -
58C THR* 2.9 28.8 + - - -
103C SER* 4.6 5.5 + - - -
122C ARG* 4.2 19.1 - - + +
123C PHE* 3.4 26.6 - + - -
124C THR* 2.7 44.2 + - - +
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Residues in contact with VAL 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA* 4.2 0.6 - - + -
32C HIS* 1.3 78.7 + - - +
34C CYS* 1.3 79.2 + - - +
46C LEU* 4.4 7.2 - - + -
49C LEU* 4.2 25.6 - - + -
54C ILE* 4.7 12.1 - - + +
56C SER 3.0 11.1 + - - +
57C PHE* 3.0 27.1 - - + -
58C THR 2.9 22.7 + - - -
123C PHE* 4.1 1.5 - - - -
125C VAL* 3.4 20.9 - - + +
127C VAL* 4.0 19.3 - - + -
505C VAL* 4.7 4.5 - - + -
509C ILE* 5.7 6.5 - - + -
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Residues in contact with CYS 34 (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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33C VAL* 1.3 82.3 - - - +
35C LEU* 1.3 59.0 + - - +
36C ILE* 4.0 13.5 - - - -
58C THR 3.3 6.7 - - - +
60C ILE* 3.7 28.5 - - - -
120C PHE* 4.3 9.0 - - - -
123C PHE* 3.5 41.3 - - + -
125C VAL 3.1 6.9 + - - +
126C VAL* 4.4 4.0 - - + -
127C VAL* 2.8 35.3 + - - +
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Residues in contact with LEU 35 (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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34C CYS* 1.3 74.3 - - - +
36C ILE* 1.3 67.9 + - - +
38C ALA* 4.3 7.4 - - - -
42C GLY* 3.3 35.9 - - - +
43C THR* 4.2 2.2 - - + +
45C ILE* 5.4 0.9 - - + -
46C LEU* 3.7 36.8 - - + -
57C PHE* 6.1 0.4 - - - +
58C THR 2.9 12.0 + - - +
59C ILE* 3.3 17.3 - - + +
60C ILE 2.6 34.1 + - - +
127C VAL* 3.3 13.7 - - + +
129C THR* 3.4 32.8 - - + -
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Residues in contact with ILE 36 (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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34C CYS* 4.0 11.4 - - - -
35C LEU* 1.3 75.7 - - - +
37C ASN* 1.3 64.5 + - - +
60C ILE* 3.2 18.2 - - + +
109C PRO* 3.3 35.7 - - + -
120C PHE* 4.6 7.4 - - + -
126C VAL* 3.7 25.6 - - + -
127C VAL 3.1 16.5 + - - +
128C ALA* 4.0 15.0 - - + -
129C THR* 2.6 34.5 + - - +
131C LEU* 3.5 20.9 - - + -
139C LEU* 4.9 5.6 - - + -
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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