Contacts of the helix formed by residues 254 - 268 (chain A) in PDB entry 5H8N
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 TRP 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASN* 4.4 17.5 - - + -
8A LEU* 3.6 34.8 - - + +
73A VAL* 3.7 35.4 - - + -
74A LYS 4.6 4.0 - - - -
75A PHE* 4.2 23.8 - + + -
108A VAL* 3.9 16.7 - - + +
109A MET* 4.4 3.6 - - + -
248A LEU* 3.8 12.8 - - + -
252A SER* 3.1 15.6 - - - +
253A PRO* 1.3 96.0 - - + +
255A LYS* 1.3 65.1 + - - +
256A ARG 3.5 0.9 - - - -
257A GLN* 3.5 8.3 + - + +
258A ILE* 3.1 31.6 + - + +
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Residues in contact with LYS 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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125A ASP* 3.8 32.5 - - + +
126A PHE 3.8 25.0 + - - +
127A SER* 4.6 0.2 - - - -
248A LEU* 4.1 20.8 - - + +
252A SER* 3.7 16.2 + - - +
253A PRO 3.6 1.8 - - - -
254A TRP* 1.3 76.0 - - - +
256A ARG* 1.3 55.9 + - - +
258A ILE* 3.0 3.0 + - - -
259A ASP* 2.8 63.9 + - - +
137B GLU* 4.9 12.3 + - - -
140B LYS* 4.9 4.8 - - - +
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Residues in contact with ARG 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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253A PRO 4.9 5.9 + - - +
254A TRP 3.5 0.4 - - - -
255A LYS* 1.3 76.5 - - - +
257A GLN* 1.3 62.1 + - - +
259A ASP* 3.5 5.6 + - - +
260A LEU* 3.1 47.7 + - + +
134B GLN* 3.1 29.5 + - - +
257B LYS* 3.4 34.4 - - - +
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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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72A THR 5.9 0.2 - - - +
73A VAL* 3.7 34.3 - - + +
253A PRO 5.3 2.2 + - - +
254A TRP* 3.5 9.6 + - + +
255A LYS 3.3 0.2 - - - -
256A ARG* 1.3 79.5 - - - +
258A ILE* 1.3 59.8 + - - +
260A LEU* 3.8 22.4 - - - +
261A ALA* 3.1 30.7 + - - +
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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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69A LEU* 4.1 12.2 - - + +
73A VAL* 4.4 18.8 - - + -
75A PHE* 5.0 5.6 - - + -
109A MET* 3.5 39.0 - - + -
127A SER* 4.1 13.5 - - - -
246A ILE* 4.3 15.5 - - + -
248A LEU* 3.8 13.9 - - + -
254A TRP* 3.1 23.5 + - + +
255A LYS* 3.0 6.9 + - - +
257A GLN* 1.3 74.8 - - - +
259A ASP* 1.4 60.5 + - - +
261A ALA* 3.3 2.9 + - - +
262A LEU* 3.0 47.1 + - + +
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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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127A SER* 3.1 29.4 - - - -
128A VAL* 3.2 33.9 + - + +
255A LYS* 2.8 48.7 + - - +
256A ARG* 3.9 5.2 - - - +
258A ILE* 1.4 71.4 - - - +
260A LEU* 1.4 57.8 + - + +
262A LEU* 3.4 2.6 + - - +
263A LEU* 3.0 38.3 + - + +
133B ALA* 6.0 2.0 - - + -
140B LYS* 5.7 0.2 + - - -
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Residues in contact with LEU 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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256A ARG* 3.1 37.5 + - + +
257A GLN* 3.8 20.9 - - - +
259A ASP* 1.4 75.5 - - + +
261A ALA* 1.3 57.3 + - - +
263A LEU* 3.4 1.4 + - - -
264A GLN* 2.9 25.9 + - - +
130B ASN* 2.9 46.2 + - - +
133B ALA* 3.8 14.4 - - + +
134B GLN* 3.6 37.9 - - + +
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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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69A LEU* 3.8 17.5 - - + -
72A THR* 3.8 27.8 - - + -
73A VAL* 3.9 5.8 - - + -
257A GLN 3.1 19.0 + - - +
258A ILE 3.8 3.6 - - - +
260A LEU* 1.3 73.9 - - - +
262A LEU* 1.4 64.8 + - - +
264A GLN* 3.2 8.3 + - - +
265A PHE* 3.0 33.3 + - + -
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Residues in contact with LEU 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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65A ILE* 3.8 30.5 - - + -
69A LEU* 4.2 11.9 - - + -
127A SER* 3.7 29.2 - - - +
128A VAL* 4.0 21.3 - - + +
130A PHE* 4.3 22.4 - - + -
246A ILE* 3.9 14.6 - - + -
258A ILE* 3.0 22.6 + - + +
259A ASP 3.8 3.6 - - - +
261A ALA* 1.4 73.7 - - - +
263A LEU* 1.4 63.2 + - - +
265A PHE* 3.2 24.0 + - + +
266A VAL* 3.2 18.3 + - + +
271A MET* 4.6 4.5 - - - +
302A 5YD 6.3 1.1 - - + -
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Residues in contact with LEU 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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128A VAL* 4.1 21.8 - - + -
259A ASP* 3.0 22.7 + - + +
260A LEU* 3.9 2.9 - - - +
262A LEU* 1.4 72.8 - - - +
264A GLN* 1.3 64.7 + - - +
266A VAL* 3.4 7.2 + - + +
267A GLY* 3.1 19.4 + - - -
302A 5YD 3.6 33.4 - - + +
128B ILE* 4.0 25.6 - - + +
129B ASN* 4.0 7.8 - - - +
130B ASN* 3.8 24.4 + - - +
133B ALA* 3.6 31.0 - - + -
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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
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72A THR* 4.1 18.0 + - - +
260A LEU 2.9 17.0 + - - +
261A ALA* 3.2 7.7 + - - +
263A LEU* 1.3 77.8 - - - +
265A PHE* 1.3 70.2 + - - +
268A ASP* 2.8 57.4 + - - +
270A GLU* 4.1 8.3 + - - -
130B ASN* 4.0 12.7 - - - +
188B ARG* 3.1 19.9 + - - +
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Residues in contact with PHE 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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65A ILE* 4.4 4.9 - - + -
68A LYS* 3.5 41.1 - - + -
69A LEU* 3.6 25.1 - - + -
72A THR* 3.6 24.5 - - + -
261A ALA* 3.0 29.8 + - + -
262A LEU* 3.2 20.6 + - + +
264A GLN* 1.3 86.9 - - - +
266A VAL* 1.3 60.9 + - - +
269A GLY 3.4 2.1 + - - -
270A GLU* 3.0 61.6 + - + -
271A MET* 3.2 22.8 + - + -
274A LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 266 (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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262A LEU* 3.2 15.8 + - + +
263A LEU* 3.4 11.9 - - + +
264A GLN 3.2 0.2 - - - -
265A PHE* 1.3 78.6 - - - +
267A GLY* 1.3 59.7 + - - +
268A ASP 3.6 0.2 + - - -
269A GLY* 3.6 8.5 + - - -
271A MET* 3.7 18.0 - - + +
302A 5YD 3.4 59.9 - - + +
128B ILE 6.0 1.1 - - - +
185B TYR* 4.8 0.7 - - - -
247B PHE* 3.4 38.3 - - + -
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Residues in contact with GLY 267 (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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263A LEU 3.1 12.5 + - - -
266A VAL* 1.3 80.2 - - - +
268A ASP* 1.4 54.1 + - - +
269A GLY 3.4 0.2 - - - -
185B TYR* 4.4 13.1 - - - -
188B ARG* 3.3 29.0 + - - +
189B GLN* 3.2 26.2 - - - +
247B PHE* 5.0 1.6 - - - -
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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
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264A GLN* 2.8 48.8 + - - +
265A PHE 4.3 1.3 - - - +
266A VAL 3.4 0.2 - - - -
267A GLY* 1.4 72.0 - - - +
269A GLY* 1.3 57.8 + - - +
270A GLU* 3.2 23.3 + - + +
188B ARG* 2.9 26.5 + - - +
189B GLN* 4.2 8.2 + - - -
191B GLU* 4.1 10.9 - - - +
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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