Contacts of the strand formed by residues 123 - 130 (chain A) in PDB entry 5T1I
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 PRO 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE* 4.2 9.9 - - + -
121A LEU 3.6 8.1 - - - +
122A ASP* 1.3 87.6 - - + +
124A GLU* 1.3 58.4 + - - +
140A MET* 3.7 23.1 - - + -
141A LYS 4.0 0.7 - - - +
142A TRP* 3.5 20.4 - - + -
143A LYS* 3.4 15.6 - - - -
159A LYS 5.4 0.9 - - - +
160A CYS* 3.7 19.5 - - + -
163A ILE* 3.4 29.9 - - + +
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Residues in contact with GLU 124 (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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122A ASP 3.5 0.2 + - - -
123A PRO* 1.3 74.1 - - - +
125A ARG* 1.3 73.0 + - + +
141A LYS* 2.8 31.1 + - + +
142A TRP 3.7 13.1 - - - +
143A LYS* 3.8 30.7 - - + +
144A ASP 4.3 3.5 + - - -
145A SER 5.5 0.2 - - - +
163A ILE* 3.8 14.2 - - - +
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Residues in contact with ARG 125 (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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124A GLU* 1.3 92.1 - - + +
126A ILE* 1.3 73.6 + - - +
127A ILE* 4.8 6.5 - - + +
140A MET* 3.9 6.6 - - - -
141A LYS* 2.9 41.9 + - + +
163A ILE* 4.1 7.0 - - - -
170A GLU* 4.8 13.9 + - - -
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Residues in contact with ILE 126 (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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125A ARG* 1.3 84.1 + - - +
127A ILE* 1.3 63.9 + - - +
128A GLY 3.4 22.2 - - - +
138A PHE* 3.6 42.6 - - + -
139A LEU 3.6 3.8 - - - +
140A MET* 3.8 22.9 - - + -
163A ILE* 3.9 11.5 + - + +
164A VAL* 3.8 32.3 - - + -
167A PHE* 3.5 37.6 - - + +
170A GLU* 4.8 4.3 - - - +
171A ARG* 4.9 1.7 + - - -
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Residues in contact with ILE 127 (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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125A ARG* 4.3 8.3 - - + +
126A ILE* 1.3 76.6 - - - +
128A GLY* 1.3 57.9 + - - +
139A LEU* 2.8 25.4 + - + +
141A LYS* 4.1 25.1 - - + +
148A ALA* 4.0 26.9 - - + -
167A PHE* 4.4 1.3 - - - -
171A ARG* 3.9 17.0 + - - -
41C TYR* 3.5 38.4 + - + +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.4 13.0 - - - +
127A ILE* 1.3 80.4 - - - +
129A ALA* 1.3 58.6 + - - -
138A PHE* 3.4 0.5 - - - -
139A LEU* 2.8 29.6 + - - +
167A PHE* 4.0 5.6 - - - -
203A UNX 3.4 13.0 - - - -
41C TYR* 3.8 18.4 - - - -
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Residues in contact with ALA 129 (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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128A GLY* 1.3 72.9 - - - +
130A THR* 1.3 65.1 + - - +
136A LEU* 4.3 4.7 - - + -
137A MET 3.3 11.2 - - - +
138A PHE* 3.8 19.3 - - + +
139A LEU 4.9 0.2 - - - +
167A PHE* 3.9 15.7 - - + -
203A UNX 3.0 9.4 - - - -
172B LEU* 5.2 3.4 - - + -
174B TRP* 3.9 20.9 - - + -
41C TYR* 3.6 2.4 - - - +
42C ARG 3.1 23.4 + - - -
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Residues in contact with THR 130 (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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129A ALA* 1.3 77.5 - - - +
131A ASP* 1.3 62.3 + - - +
132A SER* 3.0 27.5 + - - +
135A GLU 3.6 1.7 - - - +
136A LEU* 4.0 3.6 - - - -
137A MET* 2.9 35.5 + - + +
150A LEU* 4.6 19.1 - - + -
174B TRP* 3.9 7.0 - - - -
40C ARG 4.1 17.5 - - - +
41C TYR* 4.6 3.1 - - + -
42C ARG* 3.9 19.0 - - - +
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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