Contacts of the helix formed by residues 251 - 261 (chain B) in PDB entry 3A4Y
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 6.0 1.3 - - - -
224B ALA* 4.2 9.2 - - - +
249B LEU* 2.7 17.5 + - - +
250B ASP* 1.3 75.9 - - - +
252B PRO* 1.3 72.4 - - - +
253B MET* 3.9 3.8 + - - +
254B ALA* 3.3 30.8 + - - +
255B GLY* 3.0 16.8 + - - -
290B VAL* 4.3 1.9 - - - +
291B VAL 3.9 3.4 + - - -
310B LEU 4.6 4.0 - - - -
311B ALA* 4.7 7.4 - - - -
312B GLY 5.1 4.1 + - - -
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Residues in contact with PRO 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 6.0 2.7 - - - +
251B SER* 1.3 82.2 - - - +
253B MET* 1.3 65.1 + - + +
255B GLY* 3.0 5.0 + - - -
256B ARG* 2.9 42.7 + - - +
290B VAL* 5.1 1.3 - - + +
291B VAL 4.0 4.9 - - - +
292B GLU* 3.4 45.2 - - - +
320B ARG* 3.7 24.5 - - - +
436B SO4 5.4 0.2 - - - +
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 6.2 1.6 - - + -
92B ILE* 3.8 21.8 - - - -
93B VAL* 4.3 25.1 - - + +
96B ASP* 3.8 40.6 - - + +
224B ALA* 3.3 23.3 - - + -
225B VAL* 4.5 13.2 - - + -
251B SER* 3.3 3.8 - - - +
252B PRO* 1.3 79.4 - - - +
254B ALA* 1.3 63.5 + - - +
256B ARG* 3.0 32.3 + - - +
257B VAL* 3.0 16.6 + - + +
440B SO4 5.2 5.2 - - - +
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ALA* 3.8 24.8 - - - +
228B ALA* 4.3 9.4 - - + -
229B GLN* 3.7 3.4 + - - +
249B LEU* 3.7 23.3 - - + -
251B SER* 3.3 28.0 + - - +
253B MET* 1.3 78.3 - - - +
255B GLY* 1.3 57.8 + - - +
257B VAL* 3.0 4.9 + - - +
258B LEU* 2.8 29.1 + - - +
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LEU* 3.8 12.0 - - - +
251B SER 3.0 10.1 + - - -
252B PRO 3.0 7.8 + - - -
254B ALA* 1.3 76.9 - - - +
256B ARG* 1.3 62.2 + - - +
258B LEU* 3.1 5.2 + - - +
259B SER* 2.9 29.8 + - - -
290B VAL* 4.2 18.2 - - - -
292B GLU* 5.8 0.2 - - - -
446B SO4 4.5 4.5 + - - -
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Residues in contact with ARG 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 3.0 42.8 + - + +
95B GLU* 6.4 0.2 - - - +
96B ASP* 3.2 30.9 + - - +
99B LYS* 4.5 20.4 - - - +
252B PRO* 2.9 30.2 + - - +
253B MET* 3.0 28.6 + - - +
255B GLY* 1.3 76.2 - - - +
257B VAL* 1.3 59.9 + - - +
259B SER* 3.8 8.1 + - - -
260B LEU* 3.6 11.3 + - - +
292B GLU* 5.6 1.2 + - - -
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 4.0 26.0 - - + -
92B ILE* 4.0 18.4 - - + -
93B VAL* 6.0 0.7 - - + -
224B ALA 4.4 6.7 - - - +
225B VAL* 3.5 15.5 - - + +
229B GLN* 3.2 25.6 - - - +
253B MET* 3.0 17.2 + - + +
254B ALA 3.0 3.4 + - - +
256B ARG* 1.3 77.9 - - - +
258B LEU* 1.3 66.2 + - - +
259B SER 3.2 0.2 - - - -
260B LEU* 3.0 12.0 + - - +
261B TYR* 3.1 35.8 + - + -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B GLN* 3.7 14.1 + - + +
232B LEU* 3.9 16.2 - - + -
249B LEU* 4.1 11.9 - - + -
254B ALA 2.8 15.5 + - - +
255B GLY* 3.5 5.2 - - - +
257B VAL* 1.3 78.8 - - - +
259B SER* 1.3 61.5 + - - +
261B TYR* 3.1 18.1 + - + +
262B PRO* 3.3 9.9 - - - +
281B ASN* 5.2 2.5 + - - +
283B PHE* 3.4 40.6 - - + +
284B ARG* 3.7 35.9 + - + +
288B LEU* 3.9 17.5 - - + -
290B VAL* 4.5 6.5 - - + -
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLY 2.9 18.2 + - - -
256B ARG* 3.8 8.8 - - - -
257B VAL 3.2 0.2 - - - -
258B LEU* 1.3 78.3 - - - +
260B LEU* 1.3 57.1 + - - +
262B PRO* 3.2 17.0 - - - +
263B ARG* 5.3 3.8 + - - +
284B ARG* 4.5 8.7 + - - +
446B SO4 3.9 20.1 + - - -
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 3.9 39.5 - - + +
89B LEU* 3.9 29.6 - - + +
92B ILE* 3.8 21.1 - - + -
256B ARG 3.6 9.1 + - - +
257B VAL* 3.0 8.8 + - + +
259B SER* 1.3 76.8 - - - +
261B TYR* 1.3 65.7 + - + +
262B PRO* 3.2 3.8 - - - -
263B ARG* 3.0 50.6 + - - +
264B LEU* 3.8 13.7 + - + +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 5.1 4.7 - - + -
143B PRO* 3.6 15.0 - - + +
170B VAL* 5.4 0.9 - - + -
225B VAL* 3.7 4.5 + - - +
226B GLU* 3.2 29.5 - - + +
229B GLN* 3.3 33.4 - - + +
257B VAL* 3.1 33.4 + - + -
258B LEU* 3.1 12.1 + - + +
260B LEU* 1.3 77.9 - - + +
262B PRO* 1.3 59.8 - - + +
264B LEU* 2.9 33.1 + - + +
265B VAL 3.6 5.4 + - - -
268B PHE* 3.3 37.6 - + + -
276B PHE* 4.4 3.3 - - - -
281B ASN* 6.0 0.2 - - - +
283B PHE* 3.5 35.7 - + + -
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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