Contacts of the helix formed by residues 254 - 267 (chain A) in PDB entry 3SN5
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 SER 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.0 18.6 - - - -
186A THR 3.5 15.1 + - - -
187A ILE* 2.8 30.2 + - - +
252A SER 3.7 1.8 + - - -
253A ILE* 1.3 77.7 - - - +
255A GLU* 1.3 64.0 + - - +
256A LEU* 3.5 10.8 + - - +
257A ILE* 3.1 17.2 + - - +
258A SER* 3.0 21.4 + - - -
136B HIS* 6.1 0.2 - - - -
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Residues in contact with GLU 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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132A THR* 3.6 15.6 - - + +
137A ALA* 3.4 28.0 - - + +
140A SER* 3.4 21.1 + - - -
141A LEU* 5.8 0.4 - - - +
253A ILE 3.8 1.8 + - - -
254A SER* 1.3 71.2 - - - +
256A LEU* 1.4 52.8 + - - +
258A SER* 3.3 5.4 + - - +
259A LEU* 2.9 36.2 + - - +
2134A UNX 2.8 24.8 - - - -
136B HIS* 3.4 41.9 + - + +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 4.5 3.8 - - + -
129A PHE* 3.7 26.7 - - + -
132A THR* 3.3 35.7 + - - +
133A LEU* 4.2 22.9 - - + -
141A LEU* 6.0 1.3 - - + -
187A ILE* 4.6 10.5 - - + -
254A SER* 3.0 9.1 - - - +
255A GLU* 1.4 76.1 - - - +
257A ILE* 1.3 66.4 + - + +
259A LEU* 3.2 4.2 + - - +
260A ARG* 2.8 45.8 + - + +
282A VAL* 3.7 23.8 - - + -
601A HEM 4.2 10.5 - - + -
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Residues in contact with ILE 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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187A ILE* 3.4 35.9 - - + +
188A PHE* 3.7 21.8 - - + -
247A LEU* 4.0 28.3 - - + -
253A ILE* 3.8 13.9 - - + -
254A SER* 3.1 3.7 + - - +
256A LEU* 1.3 76.0 - - + +
258A SER* 1.4 61.1 + - - +
260A ARG* 3.6 5.7 - - + +
261A MET* 2.7 35.3 + - + +
279A HIS* 3.8 17.5 - - - +
282A VAL* 3.7 31.4 - - + -
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Residues in contact with SER 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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253A ILE* 3.8 16.1 + - - +
254A SER 3.0 15.7 + - - -
255A GLU* 3.3 12.1 + - - -
257A ILE* 1.4 76.3 - - - +
259A LEU* 1.4 62.1 + - - +
261A MET* 3.4 11.6 + - - +
262A PHE* 3.1 22.9 + - - +
134B GLN* 3.6 5.4 + - - +
135B GLY* 3.4 30.4 - - - -
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Residues in contact with LEU 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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128A THR* 4.2 20.9 - - + +
131A LYS* 4.5 11.2 - - + -
132A THR* 3.8 20.4 - - + -
255A GLU 2.9 20.1 + - - +
256A LEU 3.7 3.1 - - - +
258A SER* 1.4 76.6 + - - +
260A ARG* 1.3 52.1 + - - +
262A PHE* 3.2 4.1 + - + +
263A LEU* 2.8 56.7 + - + +
130B ILE* 3.8 29.6 - - + -
131B LYS* 6.0 0.4 - - - -
134B GLN* 3.5 25.1 + - + +
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Residues in contact with ARG 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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123A GLU* 2.7 40.2 + - - -
125A ILE* 5.0 0.8 - - - +
128A THR* 3.7 18.4 - - + -
129A PHE* 4.6 4.5 - - - -
256A LEU* 2.8 33.5 + - + +
257A ILE* 3.6 10.1 - - + +
259A LEU* 1.3 72.7 - - - +
261A MET* 1.4 55.3 + - - +
263A LEU* 4.6 2.2 - - - +
264A ASN* 2.8 58.8 + - - +
270A PHE* 6.0 1.2 - - - -
278A THR* 3.1 33.5 + - - +
279A HIS* 4.0 16.6 + - + +
282A VAL* 4.5 12.1 - - - -
1429A K2B 3.7 25.2 - - - +
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Residues in contact with MET 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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244A HIS* 3.3 67.7 - - + +
247A LEU* 3.9 26.0 - - + -
248A GLN* 4.2 12.3 - - + +
253A ILE* 4.9 8.7 - - + -
257A ILE* 2.7 30.0 + - - +
258A SER* 3.7 9.4 - - - +
259A LEU 3.2 0.2 - - - -
260A ARG* 1.4 69.4 - - - +
262A PHE* 1.3 66.6 + - - +
264A ASN 3.3 1.2 + - - -
265A ASP* 3.2 22.5 + - - +
279A HIS* 3.6 11.7 - - + +
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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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258A SER 3.1 11.2 + - - +
259A LEU* 3.5 8.1 - - + +
261A MET* 1.3 77.6 - - - +
263A LEU* 1.4 58.4 + - + +
265A ASP* 3.2 6.4 + - - +
266A THR* 2.9 40.7 + - + -
130B ILE* 3.4 46.9 - - + -
133B LEU* 4.2 4.7 - - + -
134B GLN* 3.5 35.7 - - + -
445B PRO* 3.6 33.7 - - + -
447B ARG* 3.8 28.9 + - - +
448B LEU* 3.9 21.3 - - + -
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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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123A GLU* 3.4 30.4 - - + +
128A THR* 3.5 26.5 - - + +
259A LEU* 2.8 40.1 + - + +
260A ARG 4.3 2.0 - - - +
262A PHE* 1.4 70.9 - - + +
264A ASN* 1.4 59.8 + - - +
266A THR* 4.4 3.1 - - - +
267A LEU* 2.8 52.5 + - + +
268A SER* 3.5 2.6 + - - -
130B ILE* 3.8 36.6 - - + -
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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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123A GLU* 4.5 0.4 - - - +
244A HIS* 3.5 24.6 + - + -
260A ARG* 2.8 45.8 + - - +
261A MET 3.3 7.6 + - - +
263A LEU* 1.4 75.0 - - - +
265A ASP* 1.4 58.9 - - - +
268A SER* 2.6 31.6 + - - +
270A PHE* 4.4 11.8 - - - -
275A LYS* 3.4 25.6 + - + +
278A THR* 3.1 24.4 + - - +
279A HIS* 3.5 8.3 + - - -
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Residues in contact with ASP 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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244A HIS* 3.5 20.6 + - - -
261A MET* 3.2 12.8 + - - +
262A PHE* 3.2 4.1 + - - +
264A ASN* 1.4 78.1 - - - +
266A THR* 1.3 59.8 + - - +
268A SER 4.2 7.0 - - - +
275A LYS* 2.8 30.9 + - - +
440B GLY 4.0 12.8 + - - +
443B ILE* 4.4 12.1 - - + +
447B ARG* 3.5 27.8 + - - +
448B LEU* 5.6 4.7 - - - +
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Residues in contact with THR 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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262A PHE* 2.9 29.9 + - + -
263A LEU* 4.4 1.1 - - - -
265A ASP* 1.3 76.7 - - - +
267A LEU* 1.3 71.5 + - + +
268A SER 3.7 0.7 - - - -
126B ASN* 4.5 9.9 - - - +
130B ILE* 3.8 28.7 - - + -
440B GLY 3.2 17.8 - - - +
441B ALA* 3.6 16.5 - - - +
443B ILE* 4.0 11.8 - - + +
445B PRO* 5.8 0.2 - - - +
447B ARG* 3.2 19.4 + - - -
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Residues in contact with LEU 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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121A THR* 3.2 27.2 - - - +
122A THR* 3.2 27.8 + - - +
123A GLU* 4.2 24.9 - - + +
263A LEU* 2.8 39.7 + - + +
266A THR* 1.3 94.2 - - + +
268A SER* 1.3 56.8 + - - +
91B HIS* 5.4 3.8 - - - +
126B ASN* 4.3 14.8 - - - +
130B ILE* 4.9 2.7 - - + -
441B ALA* 5.9 4.7 - - + -
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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