Contacts of the strand formed by residues 143 - 149 (chain B) in PDB entry 3NTV
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 TYR 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ASN* 3.7 14.8 - - + +
75B ILE 3.6 30.5 - - - -
76B LEU* 3.7 24.9 - - + -
97B HIS* 4.7 1.3 - + - -
99B THR* 3.5 11.3 + - - -
125B ARG* 3.1 21.0 + - - -
138B VAL* 2.8 33.5 + - - +
141B LYS* 3.6 29.3 - - + +
142B VAL* 1.3 73.9 - - - +
144B ASP* 1.4 62.5 + - - +
145B MSE 4.0 11.0 - - - +
146B ILE* 4.7 4.0 - - + -
165B LEU* 2.9 32.2 + - + +
166B LEU* 3.4 7.6 - - + +
167B LYS* 2.9 28.9 + - - +
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Residues in contact with ASP 144 (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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71B ASN 4.5 1.7 - - - +
72B VAL* 4.0 24.8 - - + +
73B LYS* 2.8 29.9 + - - +
74B ASN* 2.8 21.8 + - - +
142B VAL* 4.9 2.5 - - - +
143B TYR* 1.4 74.9 - - - +
145B MSE 1.4 59.9 + - - +
166B LEU* 3.5 5.4 - - - -
167B LYS* 3.3 39.6 + - - +
170B GLY* 3.4 5.7 - - - -
171B LEU* 3.1 22.2 + - - +
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Residues in contact with MSE 145 (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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63B ILE* 3.9 19.7 - - + -
66B LEU* 4.3 7.0 - - + -
67B ILE* 3.8 32.5 - - + -
72B VAL* 4.0 17.9 - - + -
74B ASN 3.4 2.1 + - - +
75B ILE* 3.4 18.0 - - + -
76B LEU 2.9 25.3 + - - -
89B PHE* 5.3 3.4 - - - -
143B TYR* 3.5 2.3 - - - +
144B ASP* 1.4 80.1 - - - +
146B ILE* 1.3 76.1 + - - +
147B PHE* 4.8 3.4 - - + +
166B LEU* 3.6 1.3 - - - +
171B LEU* 3.2 38.1 - - + +
173B ILE* 3.8 18.6 - - + -
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Residues in contact with ILE 146 (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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76B LEU* 3.2 25.1 - - + +
78B ILE* 4.5 8.1 - - + -
143B TYR* 4.7 4.0 - - + -
145B MSE 1.3 80.5 - - - +
147B PHE* 1.3 62.0 + - - +
148B ILE* 3.7 29.8 - - + -
162B TYR* 3.5 38.6 - - + +
163B THR* 3.8 16.8 - - + +
165B LEU* 5.3 0.9 - - + -
166B LEU* 3.9 22.2 - - + +
171B LEU 2.9 8.8 + - - +
172B VAL* 3.4 8.4 - - + +
173B ILE* 2.8 28.1 + - - +
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Residues in contact with PHE 147 (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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55B VAL* 3.7 34.5 - - + -
63B ILE* 3.7 26.5 - - + -
75B ILE* 5.1 3.6 - - + -
76B LEU 2.8 12.8 + - - +
77B GLU* 3.2 34.0 - - + -
78B ILE* 2.9 29.6 + - - +
85B SER* 4.1 0.4 - - - -
89B PHE* 3.8 22.2 - + + -
145B MSE 4.3 4.9 - - + -
146B ILE* 1.3 72.3 - - - +
148B ILE* 1.3 64.2 + - - +
173B ILE* 3.4 25.8 - - + -
175B ASP* 3.9 25.8 - - + -
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Residues in contact with ILE 148 (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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78B ILE* 4.0 17.9 - - + -
146B ILE* 3.7 23.3 - - + -
147B PHE* 1.3 80.1 - - - +
149B ASP* 1.3 68.9 + - - +
150B ALA 4.5 0.4 - - - +
155B SER* 4.4 19.5 - - - +
158B PHE* 4.4 11.7 - - + -
159B PHE* 3.9 35.9 - - + +
163B THR* 5.5 0.7 - - + -
172B VAL* 3.9 17.3 - - + -
173B ILE 2.9 9.4 + - - +
174B THR* 3.2 9.1 - - + +
175B ASP* 2.8 33.5 + - - +
204B TYR* 4.4 8.3 - - - +
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Residues in contact with ASP 149 (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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78B ILE* 4.7 5.5 + - - +
148B ILE* 1.3 82.6 - - - +
150B ALA* 1.4 62.1 + - - +
151B ALA* 3.0 17.5 + - - +
152B LYS* 3.2 58.4 + - + +
155B SER* 3.6 5.0 - - - -
158B PHE* 5.7 0.2 - - - -
175B ASP* 3.5 12.3 - - + +
176B ASN* 3.5 28.8 + - - +
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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