Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 1W57
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 CYS 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASP* 1.3 78.3 + - - +
120A ILE* 1.3 74.5 + - - +
121A THR* 4.8 0.7 - - - -
149A GLN* 4.4 4.5 - - - -
150A ILE 3.1 6.7 - - - -
151A SER* 3.5 20.0 - - - +
169A ASP* 4.1 4.7 - - - -
170A SER* 3.6 37.7 - - - -
173A ILE* 3.8 10.5 - - + -
179A LYS 3.4 2.2 + - - +
180A ILE* 3.6 17.4 - - + +
181A TRP 3.0 24.4 + - - -
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Residues in contact with ILE 120 (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 LEU* 3.6 36.2 - - + +
113A ASN* 3.6 21.8 - - + +
114A LEU* 4.1 12.6 - - + +
117A ALA 3.9 23.8 - - - +
118A ASP 4.8 0.9 - - - -
119A CYS* 1.3 80.8 - - - +
121A THR* 1.3 62.4 + - - +
149A GLN* 3.2 9.2 - - - +
150A ILE* 2.7 52.0 + - + +
181A TRP* 3.4 33.7 - - + -
183A VAL* 4.4 3.8 - - + -
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Residues in contact with THR 121 (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 LEU* 3.8 3.6 - - - +
119A CYS* 4.8 1.1 - - - -
120A ILE* 1.3 76.5 - - - +
122A PRO* 1.3 75.0 + - - +
145A ILE* 3.4 6.5 - - + +
146A GLN 3.6 0.3 + - - -
149A GLN* 2.6 32.1 + - - -
170A SER* 4.3 9.4 - - - -
180A ILE* 4.2 10.1 - - + -
181A TRP 2.9 14.2 + - - +
182A PHE* 3.4 31.8 - - + -
183A VAL* 2.7 32.1 + - - +
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Residues in contact with PRO 122 (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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106A LEU* 4.0 27.1 - - + -
110A LEU* 3.8 10.5 - - + -
121A THR* 1.3 94.3 + - - +
123A ALA* 1.3 60.8 + - - +
145A ILE* 3.8 1.7 - - - +
146A GLN* 3.0 38.3 + - + +
147A THR 3.8 10.5 - - - +
148A PRO 2.8 30.3 - - - +
183A VAL* 3.1 11.0 - - + +
185A GLY* 3.8 15.7 - - - -
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Residues in contact with ALA 123 (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 PRO* 1.3 74.9 - - - +
124A LEU* 1.3 64.2 + - - +
143A LYS* 4.1 12.3 - - + -
144A LEU 3.2 12.1 - - - +
145A ILE* 3.9 16.8 - - + -
146A GLN* 4.7 1.1 - - - +
182A PHE* 4.0 20.4 - - + -
183A VAL 2.8 9.1 + - - +
184A GLU* 3.5 9.5 - - - +
185A GLY* 2.8 20.4 + - - +
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Residues in contact with LEU 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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123A ALA* 1.3 76.6 - - - +
125A LYS* 1.3 68.7 + - - +
143A LYS* 3.8 5.7 - - - -
144A LEU* 2.9 45.5 + - + +
146A GLN* 3.1 33.9 - - + +
184A GLU* 4.0 15.9 - - - +
185A GLY* 3.6 28.3 - - - +
186A GLU* 3.8 8.7 - - - +
187A GLU* 4.1 17.7 - - - +
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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