Contacts of the strand formed by residues 145 - 151 (chain A) in PDB entry 3W31
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 HIS 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.4 19.5 - - + +
139A SER* 3.7 1.0 - - - -
140A ILE* 2.8 45.7 + - + +
143A ALA 3.1 0.8 - - - -
144A THR* 1.3 77.6 + - + +
146A TRP* 1.3 95.0 + - - +
147A ILE* 4.5 2.9 - - + -
160A ASP* 2.9 27.5 + - - -
162A GLN* 3.8 18.2 - - + -
163A THR* 5.8 1.1 - - + +
168A ASN* 4.2 7.1 + - - -
170A TYR* 3.1 60.7 - + + -
100B GLN* 4.3 2.5 - - - +
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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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62A ALA* 4.0 5.3 - - + +
63A SER* 3.7 39.6 - - - +
66A ALA* 3.9 18.0 - - + +
94A PHE* 3.8 21.3 - + - -
95A PHE* 4.2 16.9 - + - -
102A ILE* 3.3 36.3 - - + -
137A MET* 3.8 32.3 - - + -
138A ILE 3.4 18.8 - - - -
139A SER* 4.1 6.5 - - - -
140A ILE* 4.4 1.1 - - - -
143A ALA* 3.8 24.4 + - - +
145A HIS* 1.3 103.8 + - - +
147A ILE* 1.3 72.6 + - - +
160A ASP* 3.9 4.9 - - - +
162A GLN* 6.0 0.2 - - - +
190A ILE* 4.1 11.9 - - + -
98B ALA* 5.0 5.2 + - - +
100B GLN* 5.7 1.3 - - - -
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Residues in contact with ILE 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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66A ALA* 4.1 8.3 - - - +
137A MET* 3.9 1.4 - - - -
138A ILE* 2.9 51.1 + - + +
140A ILE* 3.6 25.4 - - + -
145A HIS* 4.2 6.3 - - + +
146A TRP* 1.3 84.5 - - - +
148A ALA* 1.3 62.1 + - - +
158A PHE* 4.7 6.5 - - + -
159A LEU 3.8 7.6 - - - +
160A ASP* 3.3 33.9 - - + +
166A GLY 5.2 1.1 - - - +
167A PHE* 4.1 25.1 - - + -
168A ASN* 3.9 20.6 - - - +
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Residues in contact with ALA 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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66A ALA* 3.7 13.8 - - - +
69A ALA* 3.3 35.0 - - + -
70A CYS* 4.1 11.0 - - - +
73A MET* 6.3 0.2 - - + -
136A VAL 3.6 4.3 - - - -
137A MET* 5.0 0.2 - - - +
138A ILE* 4.4 2.7 - - - -
147A ILE* 1.3 72.9 - - - +
149A GLY* 1.3 60.4 + - - +
157A MET 3.6 1.6 - - - +
158A PHE* 3.4 4.2 - - - -
159A LEU* 2.8 46.9 + - + +
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Residues in contact with GLY 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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126A ILE* 5.4 0.4 - - - -
135A VAL* 3.1 9.0 - - - +
136A VAL* 2.8 53.1 + - - -
138A ILE* 3.9 14.2 - - - +
148A ALA* 1.3 75.5 - - - +
150A PHE* 1.3 60.5 + - - -
156A ILE* 4.9 3.6 - - - -
157A MET 3.7 3.8 - - - -
158A PHE* 4.7 3.1 - - - -
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Residues in contact with PHE 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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25A LYS* 5.8 4.0 - - - -
28A LEU* 4.6 18.8 - - + -
73A MET* 3.7 44.4 - - + -
126A ILE* 5.6 0.9 - - - -
133A GLY* 3.5 30.5 - - - -
134A SER 3.4 11.9 - - - -
135A VAL* 3.5 12.1 - - + -
149A GLY* 1.3 74.0 - - - +
151A ASN* 1.3 67.6 + - - +
152A ASP* 3.8 24.2 + - + -
156A ILE* 3.3 9.2 - - - +
157A MET* 2.8 57.2 + - + +
159A LEU* 4.3 12.8 - - + -
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Residues in contact with ASN 151 (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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126A ILE* 4.2 3.1 - - + +
127A LEU* 3.5 10.7 - - - +
130A THR* 2.5 47.6 + - - +
131A SER 3.6 7.7 - - - +
132A LYS 3.3 11.6 - - - +
133A GLY* 3.3 13.5 - - - -
134A SER* 3.0 15.3 + - - +
150A PHE* 1.3 75.4 - - - +
152A ASP* 1.3 59.6 + - - +
153A GLY* 2.9 37.4 + - - +
155A LYS 4.1 0.7 - - - -
156A ILE* 3.1 28.0 - - + +
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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