Contacts of the helix formed by residues 269 - 277 (chain A) in PDB entry 1NVP
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 ARG 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268A ILE* 1.3 70.1 - - - +
270A LEU* 1.3 65.9 + - - +
271A GLU 3.4 2.2 - - - -
272A GLY* 3.2 8.8 + - - +
273A LEU* 3.0 20.4 + - - +
333A LYS 5.2 0.2 + - - -
334A GLY 3.6 16.6 + - - -
335A PHE* 2.9 50.6 + - + +
336A ARG* 2.9 26.7 + - - +
337A LYS* 3.8 22.0 - - + +
338A THR* 5.3 8.1 + - - +
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Residues in contact with LEU 270 (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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268A ILE* 3.1 25.5 + - + +
269A ARG* 1.3 69.0 - - - +
271A GLU* 1.3 68.4 + - - +
273A LEU* 2.9 9.2 + - + +
274A VAL* 2.9 22.2 + - - +
283A TYR* 3.4 47.3 - - + +
289A PRO 3.8 13.5 - - - +
291A LEU* 3.6 15.5 - - + +
304A ILE* 3.9 28.5 - - + +
305A PHE 4.1 9.2 - - - -
306A VAL* 3.8 23.3 - - + +
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Residues in contact with GLU 271 (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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269A ARG 3.4 0.4 - - - -
270A LEU* 1.3 78.3 - - - +
272A GLY* 1.3 60.6 + - - +
274A VAL* 3.2 15.0 - - - +
275A LEU* 3.1 58.3 + - + +
283A TYR* 3.8 22.0 - - + +
285A PRO* 5.2 3.6 - - - +
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Residues in contact with GLY 272 (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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269A ARG* 3.2 13.9 + - - +
270A LEU 3.0 1.2 - - - -
271A GLU* 1.3 78.9 - - - +
273A LEU* 1.3 63.2 + - - +
275A LEU* 3.3 9.3 + - - +
276A THR* 3.2 21.9 + - - +
335A PHE* 3.4 19.6 - - - -
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Residues in contact with LEU 273 (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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268A ILE* 4.8 7.4 - - + -
269A ARG 3.0 12.4 + - - +
270A LEU* 2.9 9.3 + - + +
272A GLY* 1.3 75.9 - - - +
274A VAL* 1.3 57.8 + - - +
276A THR* 3.3 0.5 + - - -
277A HIS* 3.0 72.7 + - + +
281A SER* 5.2 0.2 - - - +
291A LEU* 4.1 26.5 - - + -
293A TYR* 4.7 9.6 - - + -
304A ILE* 4.9 6.5 - - + -
328A ILE* 5.7 0.4 - - + -
331A ILE* 3.6 16.6 - - + -
332A LEU* 3.9 26.5 - - + -
335A PHE* 3.4 20.9 - - + -
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Residues in contact with VAL 274 (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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270A LEU 2.9 10.9 + - - +
271A GLU* 3.2 33.2 - - - +
273A LEU* 1.3 77.6 - - - +
275A LEU* 1.3 67.3 + - + +
278A GLN* 3.3 22.9 + - - +
281A SER* 3.7 22.0 - - - +
282A SER* 4.0 6.7 - - - +
283A TYR* 3.8 33.7 - - + +
291A LEU* 3.7 13.4 - - + +
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Residues in contact with LEU 275 (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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271A GLU* 3.1 48.5 + - + +
272A GLY* 3.6 9.0 - - - +
273A LEU 3.3 0.2 - - - -
274A VAL* 1.3 82.1 - - + +
276A THR* 1.3 62.2 + - + +
278A GLN* 3.2 17.4 + - - +
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Residues in contact with THR 276 (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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272A GLY 3.2 11.5 + - - +
273A LEU 3.3 1.6 + - - -
275A LEU* 1.3 79.6 - - + +
277A HIS* 1.3 92.3 + - - +
278A GLN* 3.4 12.3 + - - +
335A PHE* 3.2 20.7 - - + -
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Residues in contact with HIS 277 (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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273A LEU* 3.0 34.5 + - + +
274A VAL 3.6 3.8 - - - -
275A LEU 3.4 0.4 - - - -
276A THR* 1.3 109.6 + - - +
278A GLN* 1.3 58.7 + - - +
279A GLN 3.2 3.6 - - - +
280A PHE* 3.1 14.8 + + + -
281A SER* 2.9 33.3 + - - +
293A TYR* 3.6 33.4 - + + -
331A ILE* 3.6 27.1 - - + +
335A PHE* 4.0 8.1 - + - -
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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