Contacts of the strand formed by residues 145 - 150 (chain A) in PDB entry 4X1V
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 TRP 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A TYR* 3.5 23.1 - - - -
122A GLN* 5.6 0.7 - - - -
126A GLU* 3.6 24.9 - - + -
141A VAL* 2.9 32.6 + - + +
142A GLU* 2.9 27.4 + - + +
143A GLU 3.8 10.5 - - - -
144A GLY* 1.3 96.0 + - - +
146A TRP* 1.3 66.2 + - - +
156A LEU* 4.1 9.6 - - + -
157A PHE* 3.4 37.9 - - - -
158A PRO* 3.5 13.7 - - + -
159A SER* 3.9 1.0 + - - -
83B PRO* 4.0 14.1 - - + -
84B MET* 2.9 29.8 + - + +
85B LYS 4.0 8.1 - - - -
86B ARG* 3.2 35.1 - - + +
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Residues in contact with TRP 146 (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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113A CYS* 4.6 1.6 - - + -
137A ILE* 3.8 33.0 - - + -
139A GLU 3.4 6.1 - - - +
140A GLU* 2.8 41.5 + - + +
144A GLY 4.3 0.2 - - - -
145A TRP* 1.3 83.7 - - - +
147A SER* 1.3 63.0 + - - +
156A LEU* 3.2 8.0 - - - +
157A PHE* 2.8 68.8 + + + -
159A SER* 3.4 26.8 + - - -
162A VAL* 3.7 20.4 - - + -
164A GLU* 4.3 30.5 - - + -
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Residues in contact with SER 147 (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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137A ILE* 3.8 6.8 - - - +
138A ASN* 2.8 45.4 + - - -
139A GLU* 2.8 27.1 + - - +
141A VAL* 4.6 4.6 - - - +
146A TRP* 1.3 75.2 - - - +
148A GLY* 1.3 58.7 + - - +
154A LEU* 4.5 12.8 - - - -
155A GLY 3.2 7.4 - - - -
156A LEU* 3.7 18.2 - - - +
157A PHE* 3.7 3.1 - - - -
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Residues in contact with GLY 148 (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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127A LEU* 3.8 4.6 - - - +
135A ILE* 4.1 3.4 - - - -
136A ASP 3.0 14.6 - - - -
138A ASN* 3.9 7.6 - - - +
147A SER* 1.3 78.0 - - - +
149A THR* 1.3 64.6 + - - -
153A LYS 3.6 0.9 - - - +
154A LEU* 3.4 4.3 - - - +
155A GLY 3.0 32.0 + - - +
157A PHE* 3.7 10.4 - - - -
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Residues in contact with THR 149 (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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134A ILE 4.5 0.9 - - - +
135A ILE* 3.4 6.5 - - - +
136A ASP* 2.8 48.7 + - - +
138A ASN* 6.0 1.1 - - + -
148A GLY* 1.3 78.6 - - - +
150A LEU* 1.3 60.8 + - - +
152A ASN* 5.5 4.3 - - - -
153A LYS 3.1 13.5 - - - +
154A LEU* 4.0 24.9 - - + -
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Residues in contact with LEU 150 (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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127A LEU* 4.1 17.4 - - + +
128A GLU 3.6 18.8 - - - +
129A LEU* 4.5 7.2 - - + -
133A ASP* 3.5 40.2 - - + +
134A ILE 3.5 25.1 - - - +
135A ILE* 4.4 10.5 - - + -
149A THR* 1.3 75.3 - - - +
151A ASN* 1.3 91.8 + - - +
152A ASN 3.2 1.3 - - - -
153A LYS* 2.9 24.7 + - - +
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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