Contacts of the strand formed by residues 225 - 230 (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 LEU 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B THR* 3.7 26.2 - - + -
62B LEU* 3.8 28.7 - - + -
63B ILE* 4.4 7.6 - - + -
66B LEU* 5.4 0.7 - - + -
173B ILE* 3.5 29.4 - - + -
174B THR 3.4 11.4 - - - +
175B ASP* 3.9 12.6 - - + +
177B VAL* 3.5 5.9 - - - +
217B ASN 4.1 0.3 - - - +
218B PHE* 3.4 2.6 - - - -
219B LEU* 2.8 37.1 + - + +
221B ILE* 4.1 20.8 + - + -
224B GLY* 1.3 72.9 - - - -
226B ALA* 1.3 63.4 + - - +
227B ILE* 4.3 15.7 - - + +
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Residues in contact with ALA 226 (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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172B VAL 3.8 0.6 - - - +
173B ILE* 3.4 7.4 - - - +
174B THR* 2.9 38.9 + - - +
177B VAL* 4.0 6.0 - - + +
208B LEU* 4.1 19.3 - - + -
216B THR* 4.2 2.2 - - + -
217B ASN 3.3 7.6 - - - +
218B PHE* 3.7 29.6 - - + +
225B LEU* 1.3 74.0 - - - +
227B ILE* 1.3 62.7 + - - +
228B SER* 4.2 0.9 - - - +
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Residues in contact with ILE 227 (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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62A LEU* 4.0 27.6 - - + -
65A GLN* 2.9 31.5 - - + +
69A MSE 5.0 4.5 - - - -
62B LEU* 4.4 7.0 - - + -
66B LEU* 3.9 24.5 - - + -
171B LEU* 4.6 16.4 - - + -
172B VAL 3.7 2.9 - - - -
173B ILE* 3.9 22.4 - - + -
216B THR* 3.2 1.3 - - - -
217B ASN* 3.0 33.3 + - - +
219B LEU* 4.3 14.4 - - + -
225B LEU* 4.3 8.7 - - + -
226B ALA* 1.3 77.3 - - - +
228B SER* 1.3 62.4 + - - +
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Residues in contact with SER 228 (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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171B LEU* 3.3 7.5 - - - +
172B VAL* 2.8 56.2 + - - +
174B THR* 5.4 0.5 + - - -
208B LEU* 3.6 18.1 - - - +
214B TYR* 4.1 14.8 - - - -
215B THR 3.3 4.3 - - - -
216B THR* 2.7 28.7 + - - +
226B ALA* 5.0 0.7 - - - +
227B ILE* 1.3 74.0 + - - +
229B ILE* 1.3 63.3 + - - +
230B LYS 3.9 0.5 + - - -
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Residues in contact with ILE 229 (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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65A GLN* 3.4 35.2 - - + +
68A ARG* 3.8 28.3 - - + -
69A MSE 3.8 18.8 - - + +
169B GLN* 4.0 38.1 - - + +
170B GLY 3.5 2.9 - - - -
171B LEU* 4.0 15.0 - - + -
214B TYR* 3.3 4.9 - - - -
215B THR* 2.8 34.6 + - - +
227B ILE* 5.1 0.7 - - + -
228B SER* 1.3 75.3 - - - +
230B LYS* 1.3 66.7 + - - +
231B GLY* 3.2 3.6 + - - +
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Residues in contact with LYS 230 (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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163B THR 2.8 27.5 + - - -
164B PRO* 4.1 9.1 + - - +
166B LEU* 2.8 32.8 + - + +
167B LYS 3.6 10.8 - - - +
168B HIS* 3.7 33.0 - - + +
169B GLN* 2.7 32.9 + - - +
170B GLY 2.9 17.9 + - - +
213B GLY 4.5 0.4 - - - +
214B TYR* 3.5 39.0 + - + +
228B SER 3.9 0.4 + - - -
229B ILE* 1.3 69.6 - - - +
231B GLY* 1.3 60.9 + - - +
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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