Contacts of the helix formed by residues 257 - 271 (chain A) in PDB entry 4CSC
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASN* 2.7 27.6 - - - +
152A SER* 3.1 31.2 + - - +
154A PHE* 4.0 10.1 - - + -
155A ALA* 4.0 13.0 - - + +
255A LEU 3.6 2.6 + - - -
256A SER* 1.3 73.1 - - - +
258A PRO* 1.3 73.5 - - + +
259A TYR* 2.7 34.1 + - - +
260A LEU* 2.9 17.6 + - - +
261A SER* 2.9 20.1 + - - -
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Residues in contact with PRO 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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154A PHE* 4.1 16.8 - - + -
171A VAL* 4.1 31.6 - - + +
174A SER* 3.4 28.9 - - - +
175A ALA 4.6 4.9 - - - +
178A LEU* 3.7 6.5 - - + +
256A SER 4.6 0.4 - - - +
257A ASP* 1.3 87.6 - - + +
259A TYR* 1.3 60.5 + - - +
261A SER* 3.3 9.3 + - - +
262A PHE* 3.0 25.8 + - - +
406A LEU* 4.2 14.2 - - + +
409A LEU* 3.9 14.1 - - + -
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Residues in contact with TYR 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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145A ILE* 3.4 25.4 - - + +
148A LEU* 3.4 42.8 - - + -
149A ASN* 3.7 14.6 - - + -
151A GLU* 4.6 7.1 + - + +
152A SER* 3.7 30.1 - - - -
153A ASN 5.3 0.2 - - - -
174A SER* 3.1 31.5 - - - -
177A ASP* 3.5 17.8 + - - +
178A LEU* 4.0 29.8 + - + -
181A LYS* 3.5 22.6 - - + -
257A ASP* 2.7 12.4 + - - +
258A PRO* 1.3 73.7 - - - +
260A LEU* 1.3 63.4 + - - +
263A ALA* 3.0 19.5 + - - +
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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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146A THR* 3.9 27.1 - - + +
149A ASN* 3.8 26.2 - - + +
251A VAL* 4.1 3.6 - - + +
256A SER* 4.2 23.6 - - - +
257A ASP* 2.9 31.3 + - - +
259A TYR* 1.3 76.5 - - - +
261A SER* 1.3 63.0 + - - +
263A ALA* 3.5 5.0 + - - +
264A ALA* 3.2 21.8 + - - +
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Residues in contact with SER 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER* 3.6 36.3 - - - -
251A VAL* 3.6 20.6 - - - +
252A GLY* 3.8 5.7 - - - -
256A SER 3.9 2.8 + - - -
257A ASP 2.9 18.9 + - - -
258A PRO* 3.3 13.5 + - - +
259A TYR 3.2 0.2 - - - -
260A LEU* 1.3 76.6 - - - +
262A PHE* 1.4 59.8 + - - +
264A ALA* 3.6 3.1 + - - +
265A ALA* 3.1 20.8 + - - +
409A LEU* 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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141A LEU* 5.0 0.7 - - + -
145A ILE* 3.5 33.2 - - + -
178A LEU* 3.7 16.2 - - + -
182A LEU* 3.8 18.8 - - + -
248A SER* 4.8 2.9 - - - -
258A PRO 3.0 18.6 + - - +
259A TYR 3.6 3.1 - - - +
261A SER* 1.4 72.2 - - - +
263A ALA* 1.3 59.5 + - - +
265A ALA* 2.9 10.3 + - + +
266A MET* 2.8 61.1 + - + +
398A GLY 3.3 23.6 - - - -
401A ARG 4.5 0.9 - - - -
402A ALA* 3.4 35.0 - - + -
405A VAL* 4.1 19.3 - - + -
406A LEU* 4.9 6.0 - - + +
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Residues in contact with ALA 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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142A SER* 3.3 27.0 + - - +
145A ILE* 4.3 4.9 - - + -
146A THR* 3.1 34.1 - - - +
259A TYR 3.0 16.2 + - - +
260A LEU* 3.7 6.1 - - - +
262A PHE* 1.3 77.6 - - - +
264A ALA* 1.3 62.8 + - - +
266A MET* 3.0 16.2 + - - +
267A ASN* 3.0 9.8 + - - -
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Residues in contact with ALA 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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247A THR* 3.5 25.7 - - + +
251A VAL* 3.9 16.4 - - + -
260A LEU 3.2 10.9 + - - +
261A SER 3.7 7.2 - - - +
263A ALA* 1.3 77.0 - - - +
265A ALA* 1.3 59.6 + - - +
267A ASN* 2.9 25.7 + - - +
268A GLY 3.2 8.3 + - - -
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Residues in contact with ALA 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 SER* 3.4 35.0 - - - +
247A THR* 3.9 6.9 - - - +
248A SER* 4.2 7.6 - - - -
261A SER 3.1 11.2 + - - +
262A PHE* 2.9 20.6 + - + +
264A ALA* 1.3 78.5 - - - +
266A MET* 1.3 67.5 + - + +
268A GLY* 2.9 4.2 + - - -
269A LEU* 2.8 24.3 + - - +
401A ARG* 6.4 0.2 - - + -
405A VAL* 5.4 3.4 - - + -
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Residues in contact with MET 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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138A MET* 3.4 20.0 - - + +
141A LEU* 3.9 15.5 - - + -
142A SER* 4.2 13.2 - - - -
145A ILE* 4.4 4.5 - - + -
244A SER* 4.7 4.9 - - - -
262A PHE* 2.8 57.5 + - + +
263A ALA* 3.0 7.8 + - - +
265A ALA* 1.3 88.1 - - + +
267A ASN* 1.3 64.9 + - - +
269A LEU* 3.3 21.0 + - + -
270A ALA* 3.0 20.8 + - - +
398A GLY* 3.5 26.9 - - - +
401A ARG* 4.9 5.2 - - + -
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Residues in contact with ASN 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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138A MET 5.1 2.0 + - - -
139A SER* 5.7 1.8 - - - +
142A SER* 2.8 36.5 + - - -
263A ALA 3.0 4.0 + - - +
264A ALA* 2.9 16.6 + - - +
266A MET* 1.3 79.1 + - - +
268A GLY* 1.3 58.4 + - - +
270A ALA* 3.6 14.8 + - - +
271A GLY* 4.0 4.0 + - - -
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Residues in contact with GLY 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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243A VAL* 3.9 21.9 - - - +
244A SER 5.2 0.4 - - - -
247A THR* 5.0 3.8 - - - -
264A ALA 3.2 7.7 + - - -
265A ALA 2.9 6.7 + - - -
267A ASN* 1.3 74.8 - - - +
269A LEU* 1.4 61.0 + - - +
270A ALA 3.0 4.5 - - - -
271A GLY* 3.0 13.5 + - - -
274A HIS* 3.5 20.1 - - - +
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Residues in contact with LEU 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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138A MET* 4.3 2.7 - - + -
244A SER* 3.9 8.1 - - - +
265A ALA 2.8 18.2 + - - +
266A MET* 3.3 19.7 + - + +
268A GLY* 1.4 71.6 - - - +
270A ALA* 1.3 58.1 + - - +
274A HIS* 3.6 28.8 - - + +
275A GLY* 2.9 45.6 + - - -
276A LEU 3.0 10.4 + - - -
394A THR* 3.7 13.1 - - + +
397A PHE* 3.7 26.5 - - + +
398A GLY* 3.3 39.5 - - - +
401A ARG* 4.7 2.7 - - + -
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Residues in contact with ALA 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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136A HIS* 5.9 0.2 - - + -
138A MET* 3.7 30.3 - - + +
266A MET 3.0 15.4 + - - +
267A ASN* 3.9 10.5 - - - +
268A GLY 3.0 0.8 - - - -
269A LEU* 1.3 77.9 - - - +
271A GLY* 1.3 62.2 + - - +
272A PRO* 3.9 1.4 - - - +
276A LEU* 3.3 27.9 - - + +
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Residues in contact with GLY 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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267A ASN 4.0 3.4 + - - -
268A GLY 3.0 14.4 + - - -
270A ALA* 1.3 79.0 - - - +
272A PRO* 1.3 64.1 - - - +
273A LEU* 3.2 3.4 - - - -
274A HIS* 2.8 27.8 + - - -
276A LEU* 3.5 8.5 + - - -
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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