Contacts of the strand formed by residues 123 - 131 (chain B) in PDB entry 4TZM
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 GLU 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 2.8 48.6 + - - +
59B ILE* 5.3 0.3 - - - +
110B LEU 3.8 1.8 - - - +
112B VAL* 2.9 46.6 + - + +
121B ALA 3.4 0.8 - - - -
122B ILE* 1.3 87.5 - - + +
124B VAL* 1.3 68.3 + - - +
125B PHE* 3.4 25.2 - - + -
186B LEU* 4.3 1.7 - - - +
189B LEU* 3.6 13.7 - - + +
247B TRP 3.3 8.3 - - - +
248B SER* 2.6 26.6 + - - +
250B SER* 3.4 4.7 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B SER* 4.4 7.4 - - - -
110B LEU 3.6 2.5 - - - +
111B VAL* 4.6 6.3 - - + -
121B ALA* 3.7 21.3 - - + -
123B GLU* 1.3 81.1 - - - +
125B PHE* 1.3 65.3 + - - +
126B SER* 4.1 8.1 - - - -
221B TYR* 3.8 38.1 - - + +
223B LEU* 3.9 11.2 - - + -
245B GLN 3.7 0.3 - - - +
246B CYS* 3.2 7.1 - - - +
247B TRP* 2.6 64.1 + - + +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 3.5 8.6 - - + -
53B VAL* 3.5 37.9 - - + -
57B ARG* 4.0 2.7 - - + -
109B SER* 3.2 2.3 - - - -
110B LEU* 2.8 51.1 + - + +
112B VAL* 5.8 1.8 - - + -
123B GLU* 3.4 32.1 - - + -
124B VAL* 1.3 73.9 - - - +
126B SER* 1.3 58.9 + - - +
178B VAL* 5.5 1.1 - - + -
181B LEU* 4.2 6.5 - - + -
182B CYS* 4.1 19.3 - - - -
186B LEU* 4.1 8.1 - - + -
232B ILE* 3.8 25.4 - - + -
244B MET* 3.9 15.0 - - + -
245B GLN 3.5 1.3 - - - -
246B CYS* 3.5 28.3 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 2.4 28.0 + - - +
109B SER* 3.3 13.7 - - - -
124B VAL* 3.9 2.6 - - - -
125B PHE* 1.3 74.1 - - - +
127B MET* 1.3 62.1 + - - +
128B LYS* 3.7 11.6 - - - +
221B TYR* 4.1 2.0 - - - -
243B HIS 3.4 1.4 - - - +
244B MET* 3.3 8.1 - - - +
245B GLN* 3.0 33.1 + - - +
247B TRP* 3.5 26.7 - - - -
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Residues in contact with MET 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 6.0 0.7 - - - +
45B ALA* 4.7 1.3 - - - +
46B ILE* 4.0 18.6 - - - -
49B VAL* 4.0 24.5 - - + -
50B PHE* 3.6 26.0 - - + -
107B GLU* 3.3 2.5 - - - -
108B ILE* 2.9 40.8 + - + +
125B PHE 4.2 0.2 + - - -
126B SER* 1.3 73.8 + - - +
128B LYS* 1.3 62.8 + - - +
129B PHE* 3.5 33.3 - - + -
174B ILE* 6.3 1.3 - - + -
235B LEU* 5.1 9.4 - - + -
242B ALA* 4.1 15.9 - - + -
243B HIS 3.3 8.3 - - - +
244B MET* 3.7 20.0 - - + -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 3.6 19.3 - - - +
107B GLU* 3.5 31.2 - - + -
126B SER* 3.7 20.4 - - - +
127B MET* 1.3 72.7 - - - +
129B PHE* 1.3 62.9 + - - +
130B ILE* 5.6 0.4 - - - -
151B PRO* 5.0 15.0 - - + +
152B HIS* 5.8 0.4 - - - -
156B LEU* 4.5 2.1 - - - +
221B TYR* 4.8 2.1 + - - -
241B ALA 3.8 0.2 - - - +
242B ALA* 3.2 6.1 - - - +
243B HIS* 2.8 46.5 + - + +
245B GLN* 4.1 20.3 + - - +
247B TRP* 4.2 13.9 - - - -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B MET* 4.3 20.2 - - + -
46B ILE* 3.7 20.2 - - + -
100B THR* 4.3 13.7 - - + -
105B LEU* 3.6 42.8 - - + +
106B LYS* 2.9 36.2 + - - +
108B ILE* 4.0 5.4 - - + -
127B MET* 3.5 44.6 - - + -
128B LYS* 1.3 72.3 - - - +
130B ILE* 1.3 69.6 + - - +
131B TYR* 4.0 16.8 - + + +
153B PHE* 5.3 0.7 - - - -
240B HIS* 5.8 2.2 - + + -
241B ALA 3.3 12.8 - - - -
242B ALA* 4.0 15.7 - - + -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS* 5.8 0.4 - - - +
128B LYS 5.5 0.4 - - - +
129B PHE* 1.3 80.8 - - - +
131B TYR* 1.3 71.5 + - - +
132B PHE* 3.8 21.1 - - + -
139B ALA* 4.3 13.9 - - + -
140B ARG 5.3 2.2 - - - +
153B PHE* 3.7 47.3 - - + +
156B LEU* 3.6 39.3 - - + -
157B ALA* 3.8 6.7 - - + +
240B HIS* 3.7 5.7 - - - +
241B ALA* 2.9 37.3 + - + +
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Residues in contact with TYR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 3.2 39.8 - - - +
103B GLY* 3.6 29.6 - - - -
105B LEU* 2.4 41.9 + - - +
106B LYS* 5.1 0.4 - - + -
129B PHE* 4.0 17.5 - + + +
130B ILE* 1.3 80.2 - - - +
132B PHE* 1.3 63.0 + - - +
139B ALA* 3.8 1.9 - - - -
140B ARG* 2.8 57.9 + - + +
202B THR* 4.0 11.4 - - + -
239B HIS 4.4 1.6 - - - -
240B HIS* 3.6 23.8 - + - -
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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