Contacts of the helix formed by residues 258 - 273 (chain A) in PDB entry 1GCA
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 ALA 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.7 14.4 - - + -
19A VAL* 3.7 28.3 - - + -
20A VAL* 3.6 30.3 - - + +
23A ALA* 5.1 0.7 - - - -
255A LEU* 5.4 0.6 - - - +
256A ASN 2.8 9.0 + - - +
257A ASP* 1.3 71.0 - - - +
259A ASN* 1.3 59.4 + - - +
261A GLN* 4.1 2.1 - - - +
262A ALA* 2.9 33.2 + - - +
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Residues in contact with ASN 259 (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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19A VAL* 4.8 6.4 - - - +
23A ALA* 4.1 18.2 - - - +
27A ASP* 4.9 0.9 - - - +
257A ASP* 3.3 7.9 + - - +
258A ALA* 1.3 82.1 - - - +
260A ASN* 1.3 60.5 + - - +
262A ALA* 3.4 4.9 + - - +
263A LYS* 3.0 28.4 + - - +
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Residues in contact with ASN 260 (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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257A ASP* 2.8 34.7 + - - +
259A ASN* 1.3 76.1 - - - +
261A GLN* 1.3 61.2 + - - +
263A LYS* 4.1 7.7 - - - +
264A ALA* 2.9 30.5 + - - +
284A TRP* 3.6 24.0 - - + -
293A VAL* 3.9 14.4 - - + +
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Residues in contact with GLN 261 (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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16A PHE* 4.4 10.8 - - - -
20A VAL* 5.4 7.0 - - + -
90A PHE* 6.2 3.6 - - + -
91A ASN* 4.9 12.0 + - - +
108A VAL* 3.6 15.0 - - + +
109A GLY* 4.0 14.4 - - - +
110A THR* 3.3 22.7 - - - +
256A ASN* 2.9 26.9 + - - +
257A ASP 3.1 27.7 + - - +
258A ALA* 4.1 3.6 - - - +
260A ASN* 1.3 74.9 - - - +
262A ALA* 1.3 60.7 + - - +
265A THR* 2.9 31.1 + - - +
293A VAL* 3.8 23.4 - - + +
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Residues in contact with ALA 262 (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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20A VAL* 3.9 8.9 - - + +
23A ALA* 3.6 27.4 - - + -
24A ILE* 3.7 29.0 - - + +
27A ASP* 3.8 4.7 - - - +
258A ALA 2.9 19.0 + - - +
259A ASN 3.6 2.0 - - - +
261A GLN* 1.3 77.3 - - - +
263A LYS* 1.3 57.1 + - - +
265A THR* 3.4 4.0 + - - -
266A PHE* 3.0 30.0 + - - +
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Residues in contact with LYS 263 (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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27A ASP* 3.7 28.2 + - - +
259A ASN 3.0 19.1 + - - +
260A ASN* 3.6 11.2 - - - +
262A ALA* 1.3 74.3 - - - +
264A ALA* 1.3 57.4 + - - +
266A PHE* 3.2 10.8 + - - +
267A ASP* 2.9 60.4 + - - +
284A TRP* 3.6 20.6 - - + -
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Residues in contact with ALA 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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108A VAL* 3.8 24.2 - - + -
260A ASN 2.9 21.4 + - - +
261A GLN* 4.6 0.4 - - - -
263A LYS* 1.3 72.0 - - - +
265A THR* 1.4 60.5 + - - +
267A ASP* 3.8 0.2 - - - +
268A LEU* 3.0 32.0 + - + +
284A TRP* 3.5 37.3 - - + +
291A VAL* 4.5 6.3 - - + -
293A VAL* 5.1 1.1 - - + -
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Residues in contact with THR 265 (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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24A ILE* 4.3 11.0 - - + -
64A ALA* 3.8 27.4 - - + -
88A VAL* 4.4 9.5 - - + +
90A PHE* 3.6 30.9 - - + +
108A VAL* 3.6 23.3 - - - +
261A GLN 2.9 19.6 + - - -
262A ALA* 3.6 7.0 - - - -
264A ALA* 1.4 74.0 - - - +
266A PHE* 1.3 57.1 + - - +
268A LEU* 4.1 1.0 - - - +
269A ALA* 3.0 29.1 + - - +
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Residues in contact with PHE 266 (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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5A ILE* 4.9 3.9 - - + +
24A ILE* 4.4 14.6 - - + -
27A ASP* 3.7 39.5 - - + +
28A GLY* 3.6 20.2 - - - -
31A ALA* 3.9 20.0 - - + -
34A VAL* 3.9 24.9 - - + -
36A LEU* 4.3 13.9 - - + -
262A ALA 3.0 17.7 + - - +
263A LYS* 3.6 9.9 - - - +
265A THR* 1.3 73.5 - - - +
267A ASP* 1.3 71.8 + - - +
269A ALA* 3.5 3.7 + - - +
270A LYS* 3.0 44.9 + - + +
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Residues in contact with ASP 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 LYS* 2.9 47.5 + - - +
264A ALA 3.8 0.4 - - - +
266A PHE* 1.3 82.0 - - - +
268A LEU* 1.3 61.8 - - - +
270A LYS* 3.8 4.0 - - - +
271A ASN* 3.1 29.4 + - - +
282A THR* 4.0 18.3 - - + +
284A TRP* 2.9 34.6 + - + +
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Residues in contact with LEU 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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88A VAL* 4.3 8.5 - - + -
106A TYR* 4.5 22.7 - - + -
107A TYR 5.5 0.2 - - - +
108A VAL* 3.9 22.0 - - + -
264A ALA 3.0 21.4 + - - +
265A THR 4.1 2.5 - - - +
267A ASP* 1.3 72.7 - - + +
269A ALA* 1.3 65.3 + - - +
271A ASN* 3.3 1.0 + - - +
272A LEU* 3.0 34.4 + - + +
278A ALA* 3.6 27.6 - - + +
279A ALA* 4.9 0.7 - - - -
284A TRP* 3.8 31.6 - - + -
286A ILE* 4.2 12.3 - - + -
289A LYS 5.8 0.2 - - - +
291A VAL* 4.0 14.6 - - + -
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Residues in contact with ALA 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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5A ILE* 4.0 26.7 - - + -
62A ALA* 3.4 12.2 - - + +
63A LEU 5.1 0.4 - - - +
64A ALA* 4.6 9.9 - - + -
88A VAL* 3.9 16.7 - - + +
265A THR 3.0 20.4 + - - +
266A PHE* 4.0 4.3 - - - +
268A LEU* 1.3 75.4 - - - +
270A LYS* 1.3 56.6 + - - +
272A LEU* 4.6 1.6 - - - -
273A ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 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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3A THR* 5.4 2.0 - - + -
5A ILE* 3.8 13.8 - - + +
31A ALA* 4.7 5.6 - - - -
33A ASP* 3.0 27.2 + - - -
34A VAL* 3.4 26.7 - - + -
266A PHE* 3.0 32.9 + - + +
267A ASP* 3.8 5.8 - - - +
269A ALA* 1.3 71.7 - - - +
271A ASN* 1.3 67.4 + - - +
273A ALA* 3.3 3.2 + - - +
274A GLU* 2.9 62.5 + - + +
276A LYS* 5.7 0.2 - - - +
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Residues in contact with ASN 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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267A ASP 3.1 16.9 + - - +
268A LEU 3.7 1.1 - - - +
270A LYS* 1.3 75.4 - - - +
272A LEU* 1.3 59.7 + - - +
274A GLU* 3.0 21.1 + - - +
276A LYS* 3.0 41.5 + - + +
277A GLY 3.3 18.4 - - - +
278A ALA 3.0 24.2 + - - +
279A ALA 3.9 1.0 - - - -
280A ASP* 2.8 33.8 + - - +
282A THR* 4.0 7.1 - - - +
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Residues in contact with LEU 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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61A LYS 4.6 0.2 - - - +
86A PRO* 3.7 35.9 - - + +
88A VAL* 3.9 18.8 - - + -
104A LYS* 5.9 3.8 - - + -
106A TYR* 3.7 39.3 - - + +
268A LEU* 3.0 22.4 + - + +
269A ALA* 3.9 2.9 - - - +
271A ASN* 1.3 77.1 - - - +
273A ALA* 1.3 59.8 + - - +
275A GLY* 3.2 12.5 + - - -
276A LYS 3.9 9.2 - - - +
277A GLY* 5.1 0.4 - - - -
278A ALA* 3.9 32.1 - - + +
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Residues in contact with ALA 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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3A THR* 3.6 26.0 - - + +
5A ILE* 4.4 3.6 - - + -
61A LYS* 3.6 42.5 - - + +
62A ALA* 3.9 8.6 - - + +
269A ALA 2.9 19.7 + - - +
270A LYS* 3.3 7.2 + - - +
272A LEU* 1.3 74.2 - - - +
274A GLU* 1.3 59.8 + - - +
275A GLY 3.3 0.9 + - - -
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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