Contacts of the strand formed by residues 98 - 100 (chain A) in PDB entry 5TIN
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 LEU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS* 4.1 11.4 - - - -
64A LEU* 3.9 14.4 - - + -
66A GLN* 3.8 31.9 - - - +
96A PRO 3.4 2.6 - - - -
97A ASP* 1.3 75.8 - - - +
99A PHE* 1.3 67.1 + - - +
100A PHE* 3.8 31.2 - - + -
156A LEU* 4.0 26.7 - - + -
157A GLU 3.3 7.2 - - - +
168A PHE* 3.7 28.2 - - + -
112B THR* 2.7 40.8 + - + +
113B THR 4.2 0.3 + - - -
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Residues in contact with PHE 99 (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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97A ASP 4.4 1.1 - - - +
98A LEU* 1.3 76.1 - - - +
100A PHE* 1.3 66.2 + - - +
101A ALA* 3.7 18.8 + - + -
156A LEU* 3.7 2.8 - - - -
157A GLU* 2.8 89.6 + - + +
159A PHE* 3.6 48.2 - + + -
63B PHE* 4.2 11.7 - + - -
111B VAL 3.5 19.7 - - - +
112B THR 4.4 0.7 - - - +
115B ASN* 3.5 17.0 - - - +
131B ARG* 3.5 33.4 - - - +
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Residues in contact with PHE 100 (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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62A ILE* 4.1 9.0 - - + -
64A LEU* 4.2 7.9 - - + -
98A LEU* 3.8 19.3 - - + -
99A PHE* 1.3 77.7 - - - +
101A ALA* 1.3 65.2 + - - +
102A ASN 3.3 1.3 - - - -
103A GLU* 3.2 33.6 + - + +
132A LEU* 3.7 28.7 - - + -
134A LEU* 3.6 36.1 - - + -
136A LEU* 4.2 7.9 - - + -
154A MET* 3.9 20.4 - - + -
155A GLN 3.2 15.5 - - - +
156A LEU* 3.8 23.6 - - + -
111B VAL* 4.5 8.0 + - + -
112B THR* 4.4 4.0 - - + -
131B ARG* 3.5 11.8 + - - -
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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