Contacts of the helix formed by residues 254 - 271 (chain A) in PDB entry 3HUU
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 ASN 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ASN* 3.1 26.0 + - - +
253A ILE* 1.3 78.9 - - - +
255A PRO* 1.3 71.4 - - - +
256A ASP* 3.2 9.3 - - - +
257A VAL* 3.1 25.9 + - + +
258A LEU* 3.2 9.7 + - - +
282A ILE* 3.9 11.5 - - + +
283A SER* 2.9 27.7 + - - -
285A GLN* 3.2 23.9 + - - +
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Residues in contact with PRO 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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39A PHE* 3.8 27.1 - - + -
42A ASP* 3.4 39.5 - - + +
43A VAL* 3.6 10.9 - - - +
236A ASN* 4.1 11.7 - - - +
237A THR 5.4 4.5 - - - +
252A ASN* 4.5 3.6 - - - +
253A ILE* 3.3 11.0 - - + +
254A ASN* 1.3 87.6 - - - +
256A ASP* 1.3 60.1 + - - +
258A LEU* 3.1 14.9 + - + +
259A GLY 2.9 24.1 + - - -
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Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.6 16.8 + - - +
45A ASN* 5.1 5.8 - - - +
46A GLY* 3.5 9.1 - - - +
49A GLN* 5.0 5.9 - - - +
254A ASN* 3.5 16.5 - - - +
255A PRO* 1.3 79.9 - - - +
257A VAL* 1.3 70.4 + - - +
259A GLY 3.4 0.3 + - - -
260A PHE* 2.9 29.6 + - - +
35B ARG* 4.5 17.0 - - - +
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Residues in contact with VAL 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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254A ASN* 3.1 19.6 + - + +
256A ASP* 1.3 92.6 - - - +
258A LEU* 1.3 58.1 + - - +
260A PHE* 4.3 7.9 - - + -
261A THR* 2.6 44.0 + - - +
282A ILE* 3.5 29.8 - - + -
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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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39A PHE* 3.9 28.7 - - + -
43A VAL* 4.5 3.4 - - + -
110A VAL* 4.5 12.7 - - + +
122A ILE* 3.8 20.0 - - + +
123A ASP* 3.7 25.8 - - - +
124A ASN* 3.5 21.3 - - - +
253A ILE* 4.0 5.6 - - + +
254A ASN 3.2 11.9 + - - +
255A PRO* 3.1 15.4 + - + +
257A VAL* 1.3 77.5 - - - +
259A GLY* 1.3 57.6 + - - +
262A ALA* 2.9 31.2 + - - +
282A ILE* 3.5 27.8 - - + +
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Residues in contact with GLY 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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43A VAL* 3.5 33.6 - - - +
47A ILE* 3.4 18.8 - - - +
255A PRO 2.9 11.0 + - - -
256A ASP 3.7 2.7 - - - -
258A LEU* 1.3 75.9 - - - +
260A PHE* 1.3 56.0 + - - +
262A ALA* 3.2 1.0 + - - -
263A GLY 2.8 31.0 + - - -
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Residues in contact with PHE 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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46A GLY* 3.4 10.6 - - - +
49A GLN* 3.7 35.9 - - + +
50A ALA* 3.8 19.1 - - - +
53A VAL* 5.6 4.7 - - + -
256A ASP 2.9 17.5 + - - +
257A VAL* 4.0 8.1 - - + +
259A GLY* 1.3 75.3 - - - +
261A THR* 1.3 66.5 + - - +
264A ASN* 3.1 56.3 + - - -
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Residues in contact with THR 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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122A ILE* 3.8 19.1 - - + -
257A VAL* 2.6 34.1 + - - +
258A LEU 3.8 3.1 - - - -
260A PHE* 1.3 81.9 - - - +
262A ALA* 1.3 54.6 + - - +
264A ASN* 3.9 3.7 - - - +
265A THR* 2.7 37.5 + - - +
280A LYS* 3.7 33.0 - - + +
282A ILE* 3.9 9.0 - - + +
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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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47A ILE* 4.9 1.6 - - + -
86A ILE* 3.9 10.5 - - + +
108A LEU* 3.6 23.6 - - + +
110A VAL* 4.0 25.8 - - + -
122A ILE* 4.3 7.2 - - + +
258A LEU 2.9 19.7 + - - +
259A GLY* 3.7 5.6 - - - +
261A THR* 1.3 76.3 - - - +
263A GLY* 1.3 62.7 + - - +
266A ILE* 3.1 24.8 + - - +
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Residues in contact with GLY 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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47A ILE* 4.4 9.0 - - - -
50A ALA* 3.8 14.8 - - - -
51A CYS* 4.8 2.5 - - - -
86A ILE* 4.3 8.2 - - - +
259A GLY 2.8 17.3 + - - -
260A PHE 3.9 1.1 - - - -
262A ALA* 1.3 78.5 - - - +
264A ASN* 1.3 61.2 + - - +
266A ILE* 3.2 13.8 - - - +
267A ILE* 3.2 24.2 - - - +
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Residues in contact with ASN 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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50A ALA* 3.7 16.4 - - - +
53A VAL* 5.3 2.3 - - - +
54A ARG* 3.1 33.4 + - - +
260A PHE* 3.1 57.8 + - - +
261A THR* 4.1 3.8 - - - +
263A GLY* 1.3 75.9 - - - +
265A THR* 1.3 58.5 + - - +
267A ILE* 3.6 1.4 + - - +
268A ASP* 2.9 36.6 + - - +
280A LYS* 6.3 0.2 - - - +
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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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108A LEU* 3.5 22.7 - - + -
120A ILE* 3.8 26.5 - - + -
122A ILE* 4.2 3.5 - - + +
261A THR* 2.7 22.2 + - - +
263A GLY 3.2 0.4 - - - -
264A ASN* 1.3 76.6 - - - +
266A ILE* 1.3 61.7 + - - +
268A ASP* 3.3 10.7 + - + +
269A VAL* 3.0 29.4 + - + +
278A ARG* 5.5 2.2 - - + -
280A LYS* 2.6 37.7 + - - +
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Residues in contact with ILE 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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23A ILE* 3.6 32.3 - - + -
51A CYS* 5.7 0.7 - - - -
84A GLY* 3.6 4.7 - - - -
85A PHE 3.1 47.8 - - - +
86A ILE* 3.7 13.7 - - + -
106A PRO* 5.5 1.6 - - + +
107A TYR* 4.9 4.9 - - - +
108A LEU* 3.8 13.2 - - + +
262A ALA 3.1 15.2 + - - +
263A GLY* 3.2 14.1 - - - +
265A THR* 1.3 74.7 - - - +
267A ILE* 1.3 70.4 + - + +
269A VAL* 3.4 8.9 + - + +
270A LEU* 3.1 28.1 + - + +
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Residues in contact with ILE 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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23A ILE* 4.9 0.9 - - + -
50A ALA 4.1 4.3 - - - +
51A CYS* 4.0 25.4 - - - -
54A ARG* 3.2 51.6 - - + +
56A TYR* 3.7 32.3 - - + -
263A GLY 3.2 21.0 + - - +
264A ASN* 3.9 2.2 - - - +
265A THR 3.3 0.4 - - - -
266A ILE* 1.3 80.7 - - + +
268A ASP* 1.3 61.0 + - - +
270A LEU* 3.2 7.1 + - - +
271A ARG* 2.8 44.0 + - - +
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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
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54A ARG* 2.6 32.5 + - - +
264A ASN* 2.9 26.3 + - - +
265A THR* 3.4 11.3 - - + +
267A ILE* 1.3 77.2 - - - +
269A VAL* 1.3 57.8 + - + +
271A ARG* 3.1 24.2 + - - +
280A LYS* 4.8 7.1 + - - -
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Residues in contact with VAL 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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106A PRO* 4.7 18.6 - - + -
107A TYR 6.1 0.7 - - - +
108A LEU* 5.9 1.6 - - + -
120A ILE* 3.5 31.9 - - + -
265A THR* 3.0 19.7 + - + +
266A ILE* 3.7 10.8 - - + +
267A ILE 3.1 0.4 - - - -
268A ASP* 1.3 77.6 - - + +
270A LEU* 1.3 64.6 + - + +
271A ARG 3.2 8.0 - - - +
272A ASN 4.5 2.6 - - - +
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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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23A ILE* 3.4 33.2 - - + -
56A TYR* 3.9 20.2 - - + +
83A ASP* 3.4 40.4 - - + +
84A GLY* 4.1 4.9 - - - +
106A PRO* 3.9 26.5 - - + -
266A ILE* 3.1 21.9 + - + +
267A ILE* 3.2 4.5 + - - +
269A VAL* 1.3 76.9 - - - +
271A ARG* 1.3 60.6 + - - +
272A ASN 5.0 0.7 - - - +
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Residues in contact with ARG 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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54A ARG* 3.0 65.7 + - - +
56A TYR* 4.4 14.1 - - - +
267A ILE* 2.8 30.7 + - + +
268A ASP* 3.1 18.7 - - - +
269A VAL 3.2 6.9 - - - +
270A LEU* 1.3 76.5 - - - +
272A ASN* 1.3 72.6 + - - +
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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