Contacts of the strand formed by residues 108 - 112 (chain A) in PDB entry 5TDC
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A GLY 4.4 6.1 - - - +
107A GLU* 1.3 80.0 - - - +
109A THR* 1.3 63.9 + - - +
110A TYR* 3.9 14.7 + - - -
125A MET* 3.7 45.2 + - + +
140A MET* 4.6 21.3 - - + -
141A HIS 3.8 4.3 - - - -
142A THR* 5.0 1.3 - - - +
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Residues in contact with THR 109 (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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103A PHE* 3.6 31.7 - - + -
107A GLU* 4.0 4.0 - - + +
108A THR* 1.3 80.1 - - - +
110A TYR* 1.3 65.2 + - - +
122A VAL* 3.2 18.6 - - - +
123A LEU 3.4 13.0 - - - +
124A CYS* 4.6 1.1 - - - -
140A MET* 3.3 6.9 - - - +
141A HIS* 2.7 53.6 + - - +
143A SER* 3.3 21.9 + - - +
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Residues in contact with TYR 110 (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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108A THR* 3.9 23.0 + - - -
109A THR* 1.3 84.7 - - - +
111A SER* 1.3 62.9 + - - +
122A VAL* 3.3 5.9 - - - -
123A LEU* 2.7 41.9 + - - +
125A MET* 4.2 20.0 - - + +
128A PHE* 3.5 68.0 - + + -
138A TYR* 4.0 16.8 - + - -
139A LYS 3.5 2.2 - - - -
140A MET* 3.8 32.7 - - + +
157A TRP* 4.5 0.2 - - - -
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Residues in contact with SER 111 (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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110A TYR* 1.3 74.7 - - - +
112A CYS* 1.3 67.1 + - - +
113A ARG 4.2 0.2 - - - -
116A ALA* 3.6 13.0 - - - +
118A ASP 4.5 0.2 + - - -
119A PRO* 4.1 16.1 + - - +
121A CYS 2.7 25.3 + - - -
122A VAL* 4.5 2.9 - - - +
128A PHE* 5.3 1.0 - - - -
133A HIS* 5.9 0.7 - - - -
138A TYR* 3.3 9.2 - - - +
139A LYS* 2.9 42.3 + - - -
141A HIS* 5.4 2.1 - - - +
157A TRP* 4.6 2.0 - - - -
2B ILE* 5.6 3.4 - - - -
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Residues in contact with CYS 112 (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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111A SER* 1.3 79.0 + - - +
113A ARG* 1.3 63.6 + - - +
114A ASP* 3.6 3.8 - - - -
115A CYS* 3.6 10.3 - - + +
116A ALA* 2.9 33.8 + - - +
133A HIS* 3.6 19.3 - - + +
136A HIS* 3.4 20.9 - - - -
137A ARG 3.9 4.9 - - - -
138A TYR* 4.2 0.9 - - - +
157A TRP* 4.0 14.5 - - + -
203A ZN 2.3 37.2 - - - -
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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
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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