Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 2CW2
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 GLY 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A HIS* 3.6 9.3 + - - -
126A GLY 3.8 2.2 + - - -
127A SER* 1.3 76.7 - - - +
129A TRP* 1.3 65.1 + - - -
144A GLY 3.2 12.1 - - - -
146A ASP 3.6 9.2 - - - -
162A ASP* 3.7 0.2 - - - +
163A VAL* 2.9 31.2 + - - +
164A TRP* 3.3 15.5 - - - +
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Residues in contact with TRP 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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76A GLN* 2.9 24.8 + - - -
79A ASN* 3.3 44.3 - - + +
80A HIS* 3.6 21.8 - + - -
83A PHE* 3.8 7.2 - - + -
124A HIS* 4.7 2.4 - - - -
128A GLY* 1.3 74.1 - - - -
130A VAL* 1.3 65.9 - - - +
131A TRP* 3.5 21.5 - - + +
143A GLN* 3.4 4.9 - - - +
144A GLY 2.8 33.6 + - - +
146A ASP 3.0 24.0 + - - -
148A GLY 4.2 4.0 - - - -
160A ASN* 3.5 29.2 - - - -
161A ILE 3.3 10.1 - - - -
162A ASP* 3.3 49.6 - - + -
163A VAL* 4.1 1.9 - - - +
164A TRP* 3.5 4.2 - - - +
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Residues in contact with VAL 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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117A PHE* 3.8 20.2 - - + +
120A ALA* 3.8 16.6 - - + +
121A ALA* 3.5 32.8 - - + +
124A HIS* 5.0 2.2 - - + -
129A TRP* 1.3 77.6 - - - +
131A TRP* 1.3 63.5 + - - +
141A ILE* 3.7 26.5 - - + -
142A VAL 3.6 4.7 - - - +
143A GLN* 4.3 8.3 - - + -
160A ASN* 3.2 6.1 - - - +
161A ILE* 2.9 45.9 + - + +
163A VAL* 4.9 5.6 - - + -
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Residues in contact with TRP 131 (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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78A TYR* 4.4 6.1 - + - -
79A ASN* 3.2 34.5 - - - -
82A PHE* 4.1 9.4 - + - -
117A PHE* 3.9 4.3 - - - -
129A TRP* 3.5 16.7 - - + +
130A VAL* 1.3 77.4 - - - +
132A LEU* 1.3 58.4 + - - +
133A ILE* 3.7 7.4 - - + -
141A ILE* 3.3 7.6 - - - +
142A VAL* 2.7 55.6 + - + +
143A GLN 4.6 0.4 - - - -
144A GLY* 4.1 9.6 - - - -
148A GLY 3.1 20.1 + - - -
149A ASN* 3.7 17.7 - - - -
150A PRO* 3.4 17.4 - - + +
157A PRO* 3.6 33.9 - - + -
159A MET 3.4 9.2 - - - -
160A ASN* 3.4 37.2 - - + -
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Residues in contact with LEU 132 (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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99A ILE* 4.5 9.0 - - + -
103A ILE* 5.0 2.2 - - + -
107A PHE* 4.3 3.4 - - + -
113A PHE* 3.8 24.7 - - + -
117A PHE* 3.8 11.0 - - + -
131A TRP* 1.3 70.5 - - - +
133A ILE* 1.3 57.5 + - - +
139A LEU* 4.2 24.7 - - + -
140A LYS 3.6 26.9 - - - +
141A ILE* 4.4 1.1 - - + +
157A PRO 3.8 0.3 - - - -
158A LEU* 2.8 49.3 + - + -
159A MET* 2.9 48.9 + - + +
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Residues in contact with ILE 133 (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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131A TRP* 3.7 17.0 - - + -
132A LEU* 1.3 72.9 - - - +
134A ALA* 1.3 67.6 + - - +
135A ASP* 4.0 9.4 - - + +
139A LEU* 3.3 9.0 - - - +
140A LYS* 2.8 54.7 + - + +
142A VAL* 4.0 7.6 - - + -
150A PRO* 2.8 40.8 - - + -
155A LYS* 3.7 22.9 - - + -
156A THR 3.4 16.6 - - - +
157A PRO* 3.7 14.8 - - + -
158A LEU* 4.1 4.9 - - - -
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Residues in contact with ALA 134 (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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133A ILE* 1.3 72.8 - - - +
135A ASP* 1.3 65.6 + - - +
137A GLY 4.9 3.4 - - - +
138A LYS 3.3 7.6 - - - +
139A LEU* 4.8 0.2 - - + -
155A LYS* 4.1 0.3 - - - +
156A THR* 2.8 43.1 + - - +
158A LEU* 3.9 9.1 - - + +
199A ALA* 5.1 2.0 - - + -
201A ILE* 3.6 39.7 - - + -
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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