Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 3DGI
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASN* 4.7 11.9 + - - +
98A LYS* 4.9 5.4 + - - +
248A PRO 3.7 2.8 + - - -
249A LEU* 1.3 73.0 - - - +
251A ASP* 1.3 65.8 + - - +
252A GLU* 3.4 10.0 + - - +
253A ASN* 2.9 40.5 + - - +
254A ILE* 2.9 25.4 + - - +
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Residues in contact with ASP 251 (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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238A LEU* 5.9 1.0 - - - +
249A LEU 5.4 0.2 - - - +
250A ASP* 1.3 75.4 - - - +
252A GLU* 1.3 63.8 + - - +
254A ILE* 3.3 17.5 + - - +
255A ARG* 3.2 39.3 + - - +
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Residues in contact with GLU 252 (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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84A ASP* 5.3 2.3 - - - +
250A ASP* 3.3 8.6 + - - +
251A ASP* 1.3 80.4 - - - +
253A ASN* 1.3 61.8 + - - +
255A ARG* 3.4 15.5 + - - +
256A TYR* 3.4 44.2 + - + +
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Residues in contact with ASN 253 (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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84A ASP* 2.8 49.4 + - - +
85A GLY 4.1 0.6 - - - +
95A ASN* 3.8 23.6 - - - +
99A ALA* 4.3 0.5 - - - +
249A LEU* 3.6 18.3 - - + +
250A ASP* 2.9 25.1 + - - +
252A GLU* 1.3 76.7 - - - +
254A ILE* 1.3 64.5 + - - +
256A TYR* 3.1 7.7 + - - +
257A GLN* 2.9 44.1 + - - +
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Residues in contact with ILE 254 (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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220A ILE* 4.7 7.6 - - + -
234A LEU* 4.9 0.7 - - + -
237A MET* 3.4 38.1 - - + +
238A LEU* 4.0 30.5 - - + +
249A LEU* 3.8 22.2 - - + +
250A ASP 2.9 20.8 + - - +
251A ASP* 3.5 18.8 - - - +
253A ASN* 1.3 76.2 - - - +
255A ARG* 1.3 62.8 + - - +
257A GLN* 3.2 9.8 + - - +
258A ILE* 3.0 39.4 + - + +
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Residues in contact with ARG 255 (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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213A ASN* 5.1 8.7 - - - +
216A VAL* 3.9 15.7 - - + +
217A ASP* 3.0 36.7 + - - +
220A ILE* 3.5 35.2 - - + +
224A LYS* 4.9 8.5 - - - +
251A ASP* 3.2 27.5 + - - +
252A GLU* 3.8 10.5 - - - +
253A ASN 3.3 0.2 - - - -
254A ILE* 1.3 76.0 - - - +
256A TYR* 1.3 62.5 + - + +
258A ILE* 3.3 4.2 + - - +
259A ILE* 3.2 33.1 + - + +
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Residues in contact with TYR 256 (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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79A ARG 5.2 0.8 + - - -
80A ASP 5.3 4.0 + - - -
81A PHE* 3.5 20.0 - - - -
82A ALA 3.4 25.3 - - - +
83A GLY* 3.6 17.3 - - - -
84A ASP* 3.5 23.3 - - - -
85A GLY* 3.9 8.7 - - - +
252A GLU* 3.4 45.3 + - + +
253A ASN* 3.1 7.5 + - - +
255A ARG* 1.3 75.9 - - + +
257A GLN* 1.3 56.1 + - - +
259A ILE* 3.5 9.0 + - + +
260A THR* 2.7 37.0 + - - -
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Residues in contact with GLN 257 (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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84A ASP 4.1 1.8 + - - -
85A GLY* 3.6 8.9 - - - -
86A LEU* 3.0 29.6 + - - +
99A ALA* 3.2 25.7 - - - +
103A LEU* 4.2 5.2 - - + -
237A MET* 3.6 19.3 - - + -
249A LEU* 4.0 15.9 - - + -
253A ASN* 2.9 47.9 + - - +
254A ILE* 3.6 6.1 - - - +
256A TYR* 1.3 72.3 - - - +
258A ILE* 1.3 62.2 + - - +
260A THR* 4.1 2.0 - - - -
261A PHE* 2.8 44.1 + - + +
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Residues in contact with ILE 258 (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 PHE* 3.8 22.8 - - + -
216A VAL* 3.9 18.2 - - + +
219A ILE* 4.4 13.7 - - + -
220A ILE* 3.5 37.7 - - + -
234A LEU* 3.9 15.0 - - + -
237A MET* 3.7 16.4 - - - -
254A ILE* 3.0 21.2 + - + +
255A ARG 3.7 5.8 - - - +
256A TYR 3.3 0.4 - - - -
257A GLN* 1.3 77.0 - - - +
259A ILE* 1.3 59.1 + - - +
261A PHE* 3.8 0.9 - - - +
262A LEU* 2.9 52.6 + - + +
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Residues in contact with ILE 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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81A PHE* 3.9 32.8 - - + +
82A ALA* 4.4 8.1 - - + -
173A PHE* 5.3 3.6 - - + -
212A MET* 4.9 16.2 - - + +
213A ASN* 3.8 27.8 - - - +
216A VAL* 3.5 22.4 - - + -
255A ARG* 3.2 23.6 + - + +
256A TYR* 3.7 9.9 - - + +
258A ILE* 1.3 78.6 - - - +
260A THR* 1.3 64.0 + - - +
262A LEU* 3.3 5.8 + - - +
263A ILE* 3.1 46.9 + - + +
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Residues in contact with THR 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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82A ALA* 3.9 16.5 - - + +
85A GLY* 3.8 12.8 - - - -
86A LEU 4.4 3.8 - - - +
87A ALA* 4.0 32.2 + - + +
88A THR* 5.0 0.2 + - - -
256A TYR 2.7 23.5 + - - -
257A GLN* 3.5 9.0 - - - -
259A ILE* 1.3 79.8 - - - +
261A PHE* 1.3 61.1 + - + +
263A ILE* 3.8 3.8 - - - +
264A ALA* 2.8 31.9 + - + +
501A HEM 4.1 19.5 - - + -
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Residues in contact with PHE 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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86A LEU* 3.8 25.4 - - + -
103A LEU* 3.6 26.9 - - + -
107A PHE* 3.5 29.6 - + - -
153A ILE* 3.6 7.5 - - + +
158A PHE* 4.1 8.3 - - + -
233A LEU* 3.4 26.7 - - + -
237A MET* 3.9 8.5 - - + -
257A GLN* 2.8 36.6 + - - +
258A ILE 4.1 1.8 - - - +
260A THR* 1.3 78.8 - - + +
262A LEU* 1.3 55.7 - - - +
264A ALA* 4.8 0.9 - - - -
265A GLY* 2.7 32.8 + - - +
401A ILE* 3.8 13.0 - - + -
501A HEM 3.7 31.9 - - + -
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.4 2.5 - - + +
153A ILE* 4.1 14.3 - - + +
154A GLY* 4.4 0.9 - - - -
158A PHE* 3.7 28.3 - - + -
162A PHE* 3.7 27.8 - - + -
173A PHE* 4.0 21.5 - - + -
215A LEU* 3.8 28.0 - - + -
216A VAL* 4.9 2.7 - - + -
219A ILE* 3.9 5.8 - - + -
258A ILE* 2.9 36.5 + - + +
259A ILE* 3.8 4.9 - - - +
260A THR 3.3 0.2 - - - -
261A PHE* 1.3 76.3 - - - +
263A ILE* 1.3 52.2 + - - +
266A HIS* 2.7 36.6 + - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL* 5.8 3.1 - - + -
81A PHE* 3.9 27.8 - - + -
82A ALA* 5.9 1.6 - - + -
173A PHE* 4.5 9.0 - - + -
177A MET* 3.9 34.3 - - + -
181A LEU* 4.5 12.3 - - + -
212A MET* 4.5 4.7 - - - -
259A ILE* 3.1 30.3 + - + +
260A THR* 3.8 4.3 - - - +
262A LEU* 1.3 75.2 - - - +
264A ALA* 1.3 68.9 + - - +
265A GLY 3.2 0.3 + - - -
266A HIS* 3.3 7.8 + - - -
267A GLU* 3.2 28.0 + - + +
437A LEU* 4.6 15.3 - - + -
503A DMS 6.0 0.7 - - + -
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ALA* 5.5 1.6 - - + -
260A THR* 2.8 24.8 + - + +
261A PHE* 4.7 0.9 - - - +
263A ILE* 1.3 75.8 - - - +
265A GLY* 1.3 61.8 + - - +
266A HIS 3.3 1.2 + - - -
267A GLU 4.1 4.3 + - - -
268A ALA 4.7 1.2 + - - -
437A LEU* 6.2 0.2 - - - -
501A HEM 3.4 41.3 - - + +
503A DMS 3.4 42.1 + - + +
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Residues in contact with GLY 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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149A THR 4.2 2.8 - - - +
153A ILE* 3.9 17.5 - - - +
261A PHE 2.7 26.2 + - - -
264A ALA* 1.3 73.4 - - - +
266A HIS* 1.3 59.0 + - - +
269A THR* 4.2 4.6 + - - -
405A PHE* 4.6 4.3 - - - -
409A GLU* 4.7 3.3 - - - +
501A HEM 3.5 38.3 - - - +
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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