Contacts of the helix formed by residues 259 - 277 (chain A) in PDB entry 1DG3
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 ASP 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP* 6.2 1.1 - - + -
240A ARG 4.3 9.3 - - - +
241A PRO 2.8 18.9 + - - +
242A VAL* 3.2 17.4 - - - -
243A HIS 3.3 23.7 + - - -
257A GLU 5.1 0.9 - - - +
258A LEU* 1.3 73.0 - - - +
260A PRO* 1.3 75.1 - - + +
261A GLU* 4.4 9.8 - - + +
262A PHE* 3.2 14.4 + - + +
263A VAL* 3.3 9.7 + - - +
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Residues in contact with PRO 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU 3.3 5.3 - - - +
259A ASP* 1.3 81.4 - - + +
261A GLU* 1.3 85.5 + - - +
263A VAL* 3.1 10.4 + - + +
264A GLN* 3.0 29.2 + - + +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 3.6 22.9 - - + +
259A ASP* 3.4 8.1 - - + +
260A PRO* 1.3 93.1 - - - +
262A PHE* 1.3 61.0 + - - +
264A GLN* 3.3 6.9 + - - +
265A GLN* 2.9 32.7 + - + +
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Residues in contact with PHE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.4 40.2 - + - -
183A ARG* 3.8 31.4 - - - -
238A PHE* 4.4 5.8 - + + -
239A ASP* 3.2 24.3 - - - +
240A ARG 3.8 14.8 - - - +
241A PRO* 3.8 19.3 - - + -
258A LEU* 3.7 30.1 - - + -
259A ASP* 3.2 11.4 + - + +
260A PRO 3.2 0.6 - - - -
261A GLU* 1.3 79.3 - - - +
263A VAL* 1.3 66.5 + - - +
265A GLN* 3.0 15.5 + - - +
266A VAL* 3.0 39.4 + - + +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 5.3 4.5 - - - +
57A LYS* 5.8 6.5 - - - +
257A GLU* 5.7 4.0 - - - +
258A LEU* 4.1 27.6 - - + +
259A ASP 3.7 13.0 - - - +
260A PRO* 3.1 10.8 + - + +
262A PHE* 1.3 80.8 - - + +
264A GLN* 1.3 68.9 + - - +
266A VAL* 3.5 6.1 + - - +
267A ALA* 3.1 26.3 + - + +
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Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 3.0 22.5 + - + +
261A GLU* 3.7 6.1 - - - +
263A VAL* 1.3 87.2 + - + +
265A GLN* 1.3 60.8 + - + +
267A ALA* 3.4 9.5 + - - +
268A ASP* 2.6 44.3 + - - +
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Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE* 5.2 2.6 - - - -
237A VAL* 3.6 20.7 + - - +
238A PHE* 3.4 23.4 - - + +
239A ASP* 2.8 51.3 + - - +
261A GLU* 2.9 24.1 + - + +
262A PHE* 3.2 18.5 - - - +
264A GLN* 1.3 73.8 - - + +
266A VAL* 1.3 60.4 + - - +
268A ASP* 3.3 8.0 + - - +
269A PHE* 3.0 26.9 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.9 9.6 - - + -
54A LEU* 4.2 14.1 - - + -
57A LYS* 3.5 40.8 - - + -
238A PHE* 3.9 16.6 - - + -
262A PHE* 3.0 46.6 + - + +
263A VAL* 3.8 6.5 - - - +
265A GLN* 1.3 76.6 - - - +
267A ALA* 1.3 59.3 + - - +
269A PHE* 3.3 2.1 + - - +
270A CYS* 3.0 28.9 + - - -
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Residues in contact with ALA 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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263A VAL* 3.1 19.8 + - + +
264A GLN* 3.6 17.9 - - - +
265A GLN 3.2 0.2 - - - -
266A VAL* 1.3 77.4 - - - +
268A ASP* 1.3 61.3 + - - +
270A CYS* 3.5 5.3 + - - +
271A SER* 2.9 35.6 + - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A PHE* 3.9 11.8 - - + -
264A GLN* 2.6 33.9 + - - +
265A GLN* 3.7 8.5 - - - +
267A ALA* 1.3 80.4 - - - +
269A PHE* 1.3 60.2 + - - +
271A SER* 4.0 6.6 - - - -
272A TYR* 3.4 20.3 + - - +
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Residues in contact with PHE 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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54A LEU* 4.2 31.2 - - + -
58A LEU* 3.9 29.2 - - + -
127A VAL* 4.2 19.1 - - + -
179A VAL* 4.3 7.0 - - + -
181A THR* 3.8 19.3 - - + -
236A PHE* 3.7 33.8 - + + -
238A PHE* 4.0 12.3 - + + -
265A GLN 3.0 13.6 + - - +
266A VAL 3.4 9.6 - - - +
267A ALA 3.1 0.2 - - - -
268A ASP* 1.3 77.3 - - - +
270A CYS* 1.3 72.9 + - - +
272A TYR* 3.1 13.2 + - - +
273A ILE* 3.1 38.4 + - + +
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Residues in contact with CYS 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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57A LYS* 3.5 39.5 - - - -
58A LEU* 3.8 27.6 - - + -
266A VAL* 3.0 22.3 + - - +
267A ALA* 4.0 5.2 - - - +
269A PHE* 1.3 81.9 - - - +
271A SER* 1.3 57.6 + - - +
273A ILE* 3.3 1.2 + - - +
274A PHE* 2.9 49.5 + - + -
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.4 17.7 + - - +
267A ALA* 2.9 22.4 + - - +
268A ASP* 4.1 6.7 - - - -
269A PHE 3.2 0.2 - - - -
270A CYS* 1.3 77.4 - - - +
272A TYR* 1.3 62.0 + - - +
274A PHE* 4.5 2.5 - - - -
275A SER* 3.0 30.7 + - - -
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Residues in contact with TYR 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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177A ASP* 5.1 5.6 + - - -
179A VAL* 4.8 7.9 - - + -
232A LYS* 5.8 4.2 - - - +
233A LYS 5.5 0.2 + - - -
234A LYS* 3.7 47.0 - - + +
236A PHE* 3.5 25.8 - + + -
268A ASP 3.4 13.1 + - - +
269A PHE 3.1 10.2 + - - +
271A SER* 1.3 79.3 - - - +
273A ILE* 1.3 67.2 + - + +
275A SER* 5.0 0.2 - - - -
276A ASN* 2.8 76.4 + - + +
277A SER* 6.1 0.2 - - - -
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Residues in contact with ILE 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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39A VAL* 5.4 0.2 - - - +
41A VAL* 3.7 22.0 - - + -
58A LEU* 3.9 20.0 - - + -
85A HIS* 4.9 2.1 + - - +
93A LEU* 5.2 4.5 - - + -
125A THR* 4.0 18.4 - - + -
127A VAL* 4.4 7.2 - - + -
179A VAL* 4.7 4.3 - - + -
269A PHE* 3.1 42.8 + - + +
270A CYS 3.8 5.2 - - - +
272A TYR* 1.3 87.0 - - + +
274A PHE* 1.3 68.5 + - + +
277A SER* 3.1 44.2 + - - +
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Residues in contact with PHE 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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57A LYS 4.3 5.2 - - - -
58A LEU* 3.4 48.5 - - + -
60A GLY* 5.3 2.7 - - - -
85A HIS* 3.3 27.0 + + + -
86A PRO* 3.6 35.2 - - + -
87A LYS* 3.4 37.5 - - + +
88A LYS* 4.7 6.1 - - - +
93A LEU* 3.7 15.3 - - + -
270A CYS* 2.9 31.0 + - + +
271A SER* 4.6 1.1 - - - -
273A ILE* 1.3 80.9 - - + +
275A SER* 1.3 59.9 + - - +
277A SER 5.2 1.2 + - - +
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Residues in contact with SER 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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87A LYS* 2.7 35.1 + - - +
88A LYS* 6.0 2.8 - - - -
271A SER 3.0 11.6 + - - -
272A TYR* 4.2 1.1 - - - -
274A PHE* 1.3 78.2 - - - +
276A ASN* 1.3 68.1 + - - +
277A SER 3.9 1.1 - - - -
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Residues in contact with ASN 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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177A ASP* 5.5 1.7 - - - +
272A TYR* 2.8 75.3 + - + +
275A SER* 1.3 84.2 - - - +
277A SER* 1.3 63.6 + - - +
278A LYS* 3.3 14.2 + - - +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.6 29.7 - - - +
41A VAL* 4.3 1.3 - - - -
85A HIS* 5.0 1.0 + - - -
88A LYS* 4.3 12.0 - - - +
124A SER* 5.2 0.4 - - - -
125A THR* 2.7 33.7 + - - +
177A ASP* 4.9 2.4 + - - -
272A TYR* 6.0 0.3 - - - -
273A ILE* 3.1 40.4 + - - +
274A PHE 5.2 1.2 - - - +
275A SER 5.3 0.7 - - - -
276A ASN* 1.3 76.5 - - - +
278A LYS* 1.3 61.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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