Contacts of the strand formed by residues 29 - 33 (chain A) in PDB entry 1TJY
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.0 9.8 + - + +
28A GLU* 1.3 77.8 - - - +
30A ILE* 1.3 63.4 + - - +
59A ASP* 3.3 26.0 - - + +
83A GLN* 2.9 31.3 + - - +
84A GLY* 3.1 22.3 + - - -
85A TYR* 3.6 42.9 - - + -
86A ASP* 2.9 39.3 + - - +
87A ALA 3.4 4.0 + - - -
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Residues in contact with ILE 30 (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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29A ARG* 1.3 78.6 - - - +
31A ALA* 1.3 66.8 + - - +
58A ILE* 3.6 37.2 - - + -
59A ASP 3.0 6.3 + - - +
60A VAL* 3.2 13.3 - - + -
61A THR 2.8 24.9 + - - -
85A TYR* 3.7 4.2 - - - -
87A ALA* 3.3 19.3 - - + +
89A ILE* 3.7 29.6 - - + -
276A VAL* 4.4 11.7 - - + +
279A ALA* 3.8 22.7 - - + -
283A LEU* 4.1 14.1 - - + -
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Residues in contact with ALA 31 (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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30A ILE* 1.3 77.5 - - - +
32A PHE* 1.3 60.2 + - - +
33A ILE* 4.1 1.8 - - + -
61A THR 3.4 4.9 - - - -
80A PHE* 3.4 49.6 - - + -
85A TYR* 3.6 5.5 - - + -
87A ALA 3.0 10.4 + - - +
88A ILE* 3.5 10.7 - - + -
89A ILE* 2.8 29.6 + - - +
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Residues in contact with PHE 32 (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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30A ILE 4.1 0.2 + - - -
31A ALA* 1.3 73.2 - - - +
33A ILE* 1.3 59.7 + - - +
45A GLY 3.6 10.3 - - - -
46A GLY* 3.6 24.7 - - - -
49A ALA* 3.6 15.3 - - + -
60A VAL* 4.1 15.9 - - + -
61A THR 2.8 12.8 + - - +
62A TYR* 3.4 29.8 - + + -
63A ASP 3.2 22.7 + - - -
89A ILE* 3.4 16.8 - - + -
115A TRP* 3.2 55.6 - + - -
272A GLY* 4.0 5.8 - - - -
275A SER* 3.3 25.6 - - - -
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Residues in contact with ILE 33 (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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32A PHE* 1.3 78.6 - - - +
34A PRO* 1.3 74.2 - - - +
63A ASP 3.4 15.7 - - - +
64A GLY* 4.5 0.9 - - - -
73A GLN* 4.1 10.3 - - + +
76A LEU* 4.1 31.4 - - + -
77A VAL* 4.1 14.1 - - + -
80A PHE* 4.1 18.2 - - + -
88A ILE* 3.7 26.9 - - + -
89A ILE 2.8 13.1 + - - +
90A VAL* 3.4 16.8 - - + -
91A SER 3.0 24.3 + - - -
115A TRP* 3.1 8.3 + - - -
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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