Contacts of the helix formed by residues 263 - 276 (chain A) in PDB entry 3N57
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 SER 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 3.8 5.2 - - - -
261A ARG 3.6 1.2 + - - -
262A GLU* 1.3 76.2 - - - +
264A LEU* 1.3 62.6 - - - +
265A ASP* 3.7 8.1 + - - +
266A ASP* 3.2 32.9 + - - +
267A LEU* 3.0 22.1 + - - +
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Residues in contact with LEU 264 (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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52A ASN* 5.3 4.5 - - - +
63A GLU* 3.7 28.7 - - + +
64A TYR 3.8 25.8 - - - +
65A ARG* 3.6 37.9 - - + +
77A LEU* 4.1 20.5 - - + +
79A SER* 3.4 31.8 + - - +
263A SER* 1.3 73.4 - - - +
265A ASP* 1.3 51.9 + - - +
267A LEU* 3.9 4.9 - - + +
268A THR* 2.4 37.5 + - - -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 2.5 38.9 + - - +
263A SER* 3.2 7.6 + - - +
264A LEU* 1.3 75.1 - - - +
266A ASP* 1.3 67.5 + - - +
268A THR* 3.4 4.8 + - - -
269A ASN* 3.2 30.0 + - - +
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 4.1 18.2 - - + +
263A SER* 3.2 24.8 + - - +
265A ASP* 1.3 76.1 - - - +
267A LEU* 1.3 60.7 + - - +
269A ASN* 3.2 15.3 + - - +
270A LEU* 2.9 30.2 + - - +
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Residues in contact with LEU 267 (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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77A LEU* 3.8 25.7 - - + +
78A ILE 3.6 30.7 - - - +
79A SER* 4.2 3.8 - - - -
158A LEU* 4.2 23.8 - - + -
258A VAL* 4.5 11.8 - - + +
260A GLY* 4.3 5.8 - - - +
262A GLU* 3.5 46.7 - - + +
263A SER 3.0 11.2 + - - +
264A LEU* 3.9 5.8 - - + +
266A ASP* 1.3 76.2 - - - +
268A THR* 1.3 58.0 + - - +
270A LEU* 3.4 9.0 + - + +
271A VAL* 3.0 33.1 + - - +
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Residues in contact with THR 268 (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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47A ILE* 4.0 21.5 - - + -
50A ILE* 5.9 0.9 - - + -
65A ARG* 3.3 15.5 + - - +
67A LEU* 3.7 27.1 - - + -
77A LEU* 3.5 11.1 - - - +
264A LEU 2.4 27.2 + - - -
265A ASP* 3.5 8.1 - - - -
266A ASP 3.2 0.2 - - - -
267A LEU* 1.3 77.2 - - - +
269A ASN* 1.3 65.6 + - - +
271A VAL* 3.3 7.3 - - - +
272A VAL* 3.2 29.8 + - - +
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Residues in contact with ASN 269 (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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44A ASN* 5.5 4.7 + - - -
265A ASP* 3.2 19.4 + - - +
266A ASP* 3.2 16.3 + - - +
268A THR* 1.3 79.0 - - - +
270A LEU* 1.3 57.4 + - - +
272A VAL* 3.5 5.1 + - - +
273A LYS* 2.8 31.7 + - - +
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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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158A LEU* 3.8 28.9 - - + -
159A GLU* 3.3 44.0 - - + +
162A LEU* 4.0 16.6 - - + -
258A VAL* 5.2 1.3 - - + -
262A GLU* 5.5 4.7 - - + +
266A ASP 2.9 16.2 + - - +
267A LEU* 3.6 13.5 - - + +
269A ASN* 1.3 74.6 - - - +
271A VAL* 1.3 67.2 + - - +
273A LYS* 3.3 12.3 + - - +
274A LEU* 3.2 35.7 + - + +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.4 12.6 - - + -
69A LEU* 4.8 3.8 - - + -
75A VAL* 4.0 26.0 - - + -
77A LEU* 3.7 20.2 - - + -
162A LEU* 5.1 2.0 - - - -
256A VAL* 4.5 8.7 - - + -
258A VAL* 4.7 8.1 - - + -
267A LEU 3.0 19.9 + - - +
268A THR* 3.3 15.3 - - - +
270A LEU* 1.3 76.5 - - - +
272A VAL* 1.3 53.5 + - + +
274A LEU 3.2 0.7 + - - -
275A PHE* 2.8 60.9 + - + +
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Residues in contact with VAL 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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44A ASN* 5.3 6.7 - - - +
46A ALA* 3.8 21.5 - - + -
47A ILE* 4.1 20.4 - - + -
67A LEU* 4.9 0.2 - - + -
69A LEU* 4.0 26.5 - - + -
268A THR* 3.2 22.3 + - + +
269A ASN* 3.8 5.4 - - - +
271A VAL* 1.3 74.9 - - + +
273A LYS* 1.3 66.9 + - - +
274A LEU 3.2 0.7 + - - -
276A SER* 2.3 43.4 + - - +
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Residues in contact with LYS 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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159A GLU* 3.1 33.4 + - - -
269A ASN 2.8 22.7 + - - +
270A LEU* 3.3 10.5 + - - +
272A VAL* 1.3 74.0 - - - +
274A LEU* 1.3 80.3 + - + +
277A GLU* 4.0 12.8 - - - +
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Residues in contact with LEU 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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159A GLU* 4.5 3.4 - - + +
162A LEU* 4.0 15.0 - - + -
163A ASP* 3.3 50.5 - - + +
166A ALA* 3.6 21.6 - - + +
170A LEU* 4.3 3.8 - - - +
270A LEU* 3.2 32.4 + - + +
272A VAL 3.1 0.4 - - - -
273A LYS* 1.3 104.1 - - + +
275A PHE* 1.3 70.5 + - + +
276A SER 3.9 0.4 - - - -
277A GLU* 3.3 22.0 - - - +
278A VAL* 5.0 0.3 - - - +
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Residues in contact with PHE 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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69A LEU* 4.4 6.7 - - + -
71A ASN* 2.9 17.8 + - - -
73A ILE* 3.6 10.9 - - + +
90A LEU* 3.8 30.1 - - + -
162A LEU* 3.5 38.6 - - + -
165A PHE* 4.2 8.7 - + - -
166A ALA* 3.8 24.2 - - + -
169A PHE* 4.4 3.1 - + - -
256A VAL* 4.3 19.7 - - + -
271A VAL* 2.8 46.3 + - + +
274A LEU* 1.3 88.1 - - + +
276A SER* 1.3 58.4 + - - +
277A GLU 3.1 6.6 + - - -
278A VAL* 3.3 24.0 + - + +
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Residues in contact with SER 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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46A ALA* 4.5 15.1 - - - +
69A LEU* 4.3 13.1 - - - +
70A ALA* 5.9 1.6 - - - -
71A ASN* 3.5 19.6 + - - +
272A VAL* 2.3 46.1 + - - +
274A LEU 3.9 0.2 - - - -
275A PHE* 1.3 75.2 - - - +
277A GLU* 1.3 58.5 + - - +
278A VAL 3.3 4.3 + - - +
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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