Contacts of the strand formed by residues 148 - 156 (chain B) in PDB entry 3NT2
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 PRO 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 4.3 6.1 - - - +
140B LEU* 3.9 25.1 - - + -
146B GLY 3.3 10.1 - - - +
147B GLU* 1.3 94.6 - - + +
149B LEU* 1.3 65.1 + - - +
150B MET 5.4 0.2 - - - +
151B ILE* 5.8 0.2 - - + -
185B VAL* 4.2 20.2 - - + +
221B ILE* 3.6 33.3 - - + +
241B ILE* 4.3 10.8 - - + -
242B VAL 3.9 6.7 - - - +
243B GLY* 4.2 3.6 - - - -
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Residues in contact with LEU 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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197A PRO* 3.7 7.2 - - + +
198A LYS* 3.6 35.2 - - + +
199A LYS 3.7 13.9 - - - +
200A SER* 4.0 3.8 - - - -
210A PRO* 4.0 13.7 - - + -
228A TYR* 3.8 31.9 - - + +
147B GLU* 3.4 12.6 - - + +
148B PRO* 1.3 79.3 - - - +
150B MET* 1.3 74.5 + - + +
221B ILE* 3.4 11.1 - - - +
222B VAL 3.1 21.7 + - - -
242B VAL 2.9 8.7 + - - +
243B GLY 3.8 16.4 - - - +
244B GLU* 3.9 12.6 - - + -
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PRO* 3.8 18.8 - - + -
210A PRO* 3.8 26.5 - - + -
212A ILE* 3.9 26.9 - - + -
226A GLU* 3.3 45.1 - - + +
228A TYR* 4.4 2.9 - - + -
149B LEU* 1.3 86.9 - - + +
151B ILE* 1.3 69.2 + - - +
152B HIS* 4.3 12.1 - - + +
221B ILE* 4.4 0.7 - - - -
222B VAL 3.3 9.2 - - - +
241B ILE* 3.6 2.1 - - - +
242B VAL* 2.9 47.7 + - + +
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Residues in contact with ILE 151 (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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148B PRO* 5.8 0.7 - - + -
150B MET* 1.3 80.5 - - - +
152B HIS* 1.3 69.6 + - - +
153B CYS* 4.6 2.0 - - + +
181B LEU* 4.1 34.1 - - + -
184B LEU* 6.1 0.2 - - + -
185B VAL* 3.8 28.5 - - + -
221B ILE* 4.4 9.6 - - + -
222B VAL 3.0 6.9 + - - +
223B ILE* 3.5 25.9 - - + -
224B ASN* 3.1 28.6 + - - +
239B CYS* 4.2 17.0 - - - -
240B GLU 3.3 9.6 - - - +
241B ILE* 4.1 18.4 - - + -
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Residues in contact with HIS 152 (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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152A HIS* 6.5 1.6 - - + -
156A ARG* 4.7 0.7 - - - -
212A ILE* 5.2 3.4 - - + -
224A ASN* 4.9 4.1 + - - -
226A GLU* 2.8 38.4 + - + -
150B MET* 4.3 17.1 - - + +
151B ILE* 1.3 71.2 + - - +
153B CYS* 1.3 62.0 + - - +
222B VAL 5.9 0.2 - - - -
224B ASN* 2.9 33.6 + - - +
238B GLN* 4.4 1.2 - - - +
239B CYS* 3.5 1.2 - - - -
240B GLU* 2.9 64.4 + - + +
242B VAL* 3.8 17.8 - - + +
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Residues in contact with CYS 153 (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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151B ILE* 4.6 1.3 - - + -
152B HIS* 1.3 74.2 - - - +
154B ALA* 1.3 62.5 + - - +
177B GLU* 4.0 24.9 - - + -
181B LEU* 4.3 18.4 - - + -
223B ILE* 4.7 3.6 - - - -
224B ASN 3.2 6.4 + - - +
225B ALA* 3.2 29.2 - - - -
226B GLU* 2.9 23.4 + - - +
238B GLN* 3.1 15.5 - - - +
239B CYS* 4.1 15.5 - - + -
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Residues in contact with ALA 154 (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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153B CYS* 1.3 76.4 - - - +
155B HIS* 1.3 61.9 + - - +
156B ARG* 3.4 40.8 - - - +
177B GLU* 4.2 6.3 - - - +
225B ALA* 5.8 0.2 - - - -
226B GLU* 3.2 17.0 - - + +
236B ASP 4.4 0.7 - - - -
237B ILE* 3.5 5.0 - - - +
238B GLN* 3.0 38.6 + - + +
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Residues in contact with HIS 155 (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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127B ARG* 3.1 20.3 + - - -
154B ALA* 1.3 72.5 - - - +
156B ARG* 1.3 69.4 + - - +
157B ASN* 5.4 2.9 - - + -
173B THR* 3.6 42.0 + - + +
174B LEU* 5.7 0.2 - - + -
176B HIS* 4.6 7.4 - + - -
177B GLU* 3.0 36.6 + - - +
226B GLU 2.8 11.5 + - - +
227B ILE* 3.5 11.9 - - + +
228B TYR 3.2 21.8 + - - +
229B VAL* 5.2 0.9 - - + +
235B TYR* 3.2 24.6 + + - -
236B ASP 3.8 2.0 - - - -
237B ILE* 3.6 9.2 - - + -
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Residues in contact with ARG 156 (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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152A HIS* 4.7 0.6 + - - -
240A GLU* 4.0 19.8 + - - -
242A VAL* 4.1 1.8 - - - +
247A ILE* 3.3 25.9 - - - +
154B ALA* 3.4 17.0 - - + +
155B HIS* 1.3 84.0 - - - +
157B ASN* 1.3 62.1 + - - +
226B GLU* 2.6 44.1 + - - +
228B TYR* 3.2 11.9 - - + +
231B CYS* 3.8 17.7 - - - -
233B TYR* 2.9 32.8 + - - +
234B GLY 4.1 0.9 - - - -
235B TYR* 3.3 12.8 - - - -
236B ASP* 2.9 46.8 + - + +
238B GLN* 4.2 12.5 - - - +
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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