Contacts of the helix formed by residues 251 - 265 (chain A) in PDB entry 4DQ6
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 4.2 11.1 + - - +
224A GLU 5.3 0.2 + - - -
225A LYS* 4.5 19.4 - - + +
249A LEU* 3.2 2.8 - - - +
250A PRO* 1.3 79.8 - - - +
252A GLU* 1.3 66.0 + - - +
253A LYS* 2.8 30.2 + - - +
254A ASP* 3.1 27.6 + - - +
255A TYR* 3.0 19.9 + - - +
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Residues in contact with GLU 252 (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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249A LEU 5.2 0.4 - - - -
250A PRO 3.7 4.6 + - - -
251A ASP* 1.3 75.4 + - - +
253A LYS* 1.3 64.7 + - + +
255A TYR* 3.6 11.0 - - + +
256A LYS* 3.0 27.9 + - - +
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Residues in contact with LYS 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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251A ASP* 2.8 16.0 + - - +
252A GLU* 1.3 82.7 - - + +
254A ASP* 1.3 62.1 + - - +
256A LYS* 3.5 6.9 + - - +
257A LEU* 3.2 31.5 + - + +
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Residues in contact with ASP 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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103A LEU* 5.2 2.1 - - + +
107A LEU* 3.8 19.7 - - + +
196A LYS* 2.5 39.0 + - - -
228A ILE* 3.5 16.3 - - + +
249A LEU* 3.6 24.5 - - + +
251A ASP* 3.1 19.5 + - + +
253A LYS* 1.3 76.8 - - - +
255A TYR* 1.3 66.5 + - - +
257A LEU* 3.2 9.1 + - - +
258A LEU* 3.0 19.6 + - - +
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Residues in contact with TYR 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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88A GLU 3.2 27.8 + - - -
89A TRP* 3.8 13.9 - - - -
90A LEU 3.7 13.7 + - - -
91A ILE* 3.4 30.1 - - + +
249A LEU* 4.0 17.2 - - + +
251A ASP 3.0 13.1 + - - +
252A GLU* 3.6 14.4 - - - +
254A ASP* 1.3 76.7 - - - +
256A LYS* 1.3 64.1 + - + +
258A LEU 3.3 0.2 + - - -
259A ASP* 2.8 54.2 + - + +
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Residues in contact with LYS 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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252A GLU 3.0 16.9 + - - +
253A LYS* 3.8 7.9 - - - +
254A ASP 3.2 0.2 - - - -
255A TYR* 1.3 82.0 - - + +
257A LEU* 1.3 60.9 + - + +
259A ASP* 3.7 3.8 - - - +
260A ASP* 2.8 58.2 + - - +
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Residues in contact with LEU 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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103A LEU* 6.2 1.6 - - + -
106A GLU* 3.9 44.2 - - + +
107A LEU* 3.7 29.8 - - + -
253A LYS 3.2 16.8 + - - +
254A ASP* 3.2 11.4 + - - +
256A LYS* 1.3 81.9 - - + +
258A LEU* 1.3 58.0 + - - +
260A ASP* 3.4 5.9 + - + +
261A ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 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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91A ILE* 3.9 10.1 - - + -
99A ALA* 4.2 3.6 - - + +
102A LEU* 3.8 26.5 - - + -
103A LEU* 3.9 34.3 - - + +
106A GLU* 5.3 1.8 - - - +
247A VAL* 3.9 37.0 - - + -
249A LEU* 4.0 8.7 - - + -
254A ASP 3.0 12.4 + - - +
257A LEU* 1.3 76.8 - - - +
259A ASP* 1.3 67.9 + - - +
261A ALA* 3.1 2.7 + - + -
262A PHE* 2.9 47.0 + - + -
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Residues in contact with ASP 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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91A ILE* 3.6 16.7 - - + +
255A TYR* 2.8 46.0 + - + +
256A LYS* 3.7 6.1 - - - +
258A LEU* 1.3 74.9 - - - +
260A ASP* 1.3 62.3 + - - +
262A PHE* 3.3 3.0 + - - -
263A THR* 3.0 24.7 + - - -
268A LYS* 3.0 32.5 + - - +
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Residues in contact with ASP 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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106A GLU* 6.5 0.2 - - - -
256A LYS* 2.8 53.7 + - - +
257A LEU* 3.8 6.6 - - + +
259A ASP* 1.3 83.4 - - - +
261A ALA* 1.3 57.3 + - - +
263A THR* 3.3 10.5 + - - +
264A ARG* 2.9 27.9 + - - +
130B ASN* 5.8 0.7 - - - +
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Residues in contact with ALA 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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102A LEU* 3.9 20.8 - - + +
106A GLU* 3.7 23.0 - - + -
257A LEU 3.0 15.3 + - - +
258A LEU* 3.1 8.0 + - - +
260A ASP* 1.3 73.9 - - - +
262A PHE* 1.3 64.2 + - - +
264A ARG* 3.2 26.5 + - - +
265A ILE* 3.1 25.8 + - - +
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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
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91A ILE* 3.7 20.2 - - + -
92A TYR 3.8 11.0 - - - -
93A SER* 3.3 31.0 - - - -
94A PRO* 4.3 3.4 - - + -
98A PRO* 5.1 4.0 - - + -
99A ALA* 4.2 11.0 - - - -
102A LEU* 3.5 19.1 - - + -
258A LEU* 2.9 46.9 + - + -
259A ASP* 3.8 7.0 - - - +
261A ALA* 1.3 77.4 - - - +
263A THR* 1.3 57.3 + - - +
265A ILE* 3.5 6.4 + - + -
266A ASP* 2.8 22.7 + - - -
267A ILE* 3.0 55.4 + - + +
268A LYS* 3.8 10.3 - - + +
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Residues in contact with THR 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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259A ASP* 3.0 11.0 + - - -
260A ASP* 3.4 14.7 + - - +
261A ALA 3.2 0.2 - - - -
262A PHE* 1.3 74.8 - - - +
264A ARG* 1.3 65.1 + - - +
266A ASP* 3.0 16.6 + - - +
268A LYS* 3.0 29.1 + - - +
97B ILE* 5.8 0.2 - - - +
130B ASN* 3.6 25.1 + - - +
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Residues in contact with ARG 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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102A LEU* 3.8 14.8 - - - +
105A ASN* 3.6 15.3 - - - +
106A GLU* 2.9 28.0 + - - +
260A ASP 2.9 13.4 + - - +
261A ALA* 3.4 25.6 + - - +
263A THR* 1.3 79.1 - - - +
265A ILE* 1.3 71.2 + - - +
266A ASP* 3.7 1.0 + - - +
97B ILE* 5.2 0.5 - - - +
101B SER* 2.7 25.9 + - - +
102B LEU* 5.5 2.2 - - - +
105B ASN* 5.6 7.5 + - - +
127B VAL* 4.2 6.8 - - - +
130B ASN* 3.5 39.7 - - + +
131B ASN* 3.6 28.0 + - - +
264B ARG* 5.1 9.7 - - - +
265B ILE* 6.2 0.2 - - - +
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Residues in contact with ILE 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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98A PRO* 6.3 2.2 - - + -
102A LEU* 3.8 28.3 - - + -
261A ALA 3.1 13.9 + - - +
262A PHE* 3.9 15.5 - - + +
264A ARG* 1.3 100.9 - - - +
266A ASP* 1.3 67.0 + - - +
267A ILE* 3.3 27.1 + - + +
98B PRO* 3.2 29.7 - - + +
101B SER* 3.8 12.8 - - - +
102B LEU* 4.3 20.2 - - + -
265B ILE* 4.1 18.4 - - + -
267B ILE* 6.0 0.2 - - + -
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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
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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