Contacts of the helix formed by residues 278 - 287 (chain B) in PDB entry 2N5T
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 VAL 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B THR* 1.3 72.8 - - + +
279B ARG* 1.3 84.3 + - + +
281B VAL* 2.8 40.5 + - + +
282B GLU* 4.1 1.2 + - - +
316B ALA* 4.3 3.1 - - - +
319B ALA* 3.6 34.1 - - + +
320B VAL* 3.6 26.1 - - + +
323B ALA* 5.0 6.8 - - + +
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Residues in contact with ARG 279 (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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277B THR* 2.6 32.4 + - + +
278B VAL* 1.3 90.8 - - + +
280B ASP* 1.3 61.6 + - - +
281B VAL 3.6 0.3 + - - -
282B GLU* 3.7 22.3 - - - +
283B GLY 4.4 1.0 + - - -
303B ASP* 2.9 32.7 + - - -
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 5.8 1.7 + - - -
274B ASN 5.1 1.1 - - - +
275B ILE* 3.3 23.8 - - + +
276B GLY* 2.7 27.9 + - - -
277B THR* 2.6 26.9 + - - +
279B ARG* 1.3 74.7 - - - +
281B VAL* 1.3 62.2 - - - +
282B GLU 3.1 2.6 + - - -
283B GLY* 3.3 5.1 + - - +
284B ALA* 3.0 21.0 + - - +
299B PHE* 5.9 0.2 - - - -
527B ALA* 5.2 1.9 - - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 4.3 15.9 - - + -
278B VAL* 2.8 29.2 + - - +
280B ASP* 1.3 75.5 - - - +
282B GLU* 1.3 66.0 + - - +
284B ALA* 3.5 8.6 - - + +
285B GLU* 2.9 36.6 + - + +
292B VAL* 5.4 0.4 - - + -
320B VAL* 4.6 2.5 - - + -
323B ALA* 3.1 39.7 - - + +
324B CYS* 3.8 24.5 - - - -
327B GLN* 6.1 0.4 - - - +
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Residues in contact with GLU 282 (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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278B VAL 4.1 1.4 + - - +
279B ARG* 3.7 15.5 + - - +
281B VAL* 1.3 82.2 - - - +
283B GLY* 1.3 57.7 + - - +
285B GLU* 3.0 8.5 + - - +
286B ARG* 2.8 56.5 + - - +
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Residues in contact with GLY 283 (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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279B ARG 4.4 1.6 + - - -
280B ASP* 3.3 8.8 + - - +
282B GLU* 1.3 76.7 + - - +
284B ALA* 1.3 62.4 + - - +
286B ARG* 3.3 20.8 + - - +
287B ASN* 2.5 37.7 + - - -
527B ALA* 3.6 6.7 - - - -
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Residues in contact with ALA 284 (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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273B ALA* 3.5 25.8 - - + -
275B ILE* 4.8 2.7 - - + -
280B ASP 3.0 13.6 + - - +
281B VAL* 3.5 13.7 - - + +
282B GLU 3.1 0.4 - - - -
283B GLY* 1.3 76.3 - - - +
285B GLU* 1.3 63.0 + - + +
287B ASN 3.4 1.4 + - - -
288B GLY 3.2 3.6 + - - -
289B ALA* 2.9 38.2 + - + +
291B GLY 6.2 0.2 - - - -
292B VAL* 5.2 5.4 - - + -
527B ALA* 3.8 10.4 - - - +
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Residues in contact with GLU 285 (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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256B LEU* 4.7 6.6 - - - +
281B VAL* 2.9 29.4 + - + +
282B GLU* 3.7 7.2 - - - +
284B ALA* 1.3 75.7 - - + +
286B ARG* 1.3 63.9 + - - +
287B ASN 3.2 0.7 + - - -
288B GLY* 3.3 11.3 + - - -
289B ALA* 5.0 4.3 - - - +
323B ALA 3.0 23.7 - - - +
324B CYS* 4.6 1.6 - - - -
327B GLN* 4.5 20.9 + - - +
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Residues in contact with ARG 286 (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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254B ALA* 5.6 3.3 - - - +
256B LEU* 5.3 5.7 - - - +
282B GLU* 2.8 49.8 + - - +
283B GLY* 3.3 36.5 - - - +
285B GLU* 1.3 78.7 - - - +
287B ASN* 1.3 65.1 + - - +
288B GLY 3.4 0.4 + - - -
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Residues in contact with ASN 287 (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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256B LEU* 5.2 1.6 - - - -
283B GLY* 2.5 31.7 + - - +
284B ALA 3.4 1.8 + - - +
285B GLU 3.2 0.2 - - - -
286B ARG* 1.3 88.3 - - - +
288B GLY* 1.3 57.8 + - - +
289B ALA 3.4 1.8 - - - -
527B ALA* 3.3 39.0 - - + +
528B ILE* 3.9 16.4 - - - +
530B ILE* 3.1 23.0 - - + +
531B PRO* 3.8 24.2 - - + +
534B LYS* 4.3 2.9 + - - -
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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