Contacts of the helix formed by residues 261 - 278 (chain B) in PDB entry 3Q84
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 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.7 19.6 - - - +
100B GLU* 5.1 3.1 - - - +
257B ASN 3.9 10.7 + - - +
258B LEU* 3.2 23.1 + - + +
260B GLU* 1.3 77.6 - - - +
262B SER* 1.3 65.1 + - - +
263B SER* 2.5 44.6 + - - +
264B TYR* 3.3 17.6 + - + +
265B ILE* 3.3 20.1 + - - +
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Residues in contact with SER 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU 3.9 3.0 + - - -
261B ASN* 1.3 77.1 - - - +
263B SER* 1.3 67.2 + - - -
264B TYR 3.4 0.2 + - - -
265B ILE* 3.4 13.8 + - - +
266B HIS* 3.1 20.0 + - - +
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Residues in contact with SER 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 5.8 2.9 - - - -
97B LEU* 4.1 17.2 - - - +
261B ASN* 2.5 18.0 + - - +
262B SER* 1.3 74.8 - - - +
264B TYR* 1.4 64.4 + - - -
266B HIS* 2.9 19.4 + - - +
267B VAL* 2.9 19.8 + - - +
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU 4.0 2.6 + - - -
257A ASN* 4.1 3.6 - - - -
258A LEU* 3.2 37.0 + - + +
259A ALA* 3.5 33.4 - - + -
264A TYR* 3.9 15.7 - + - -
94B VAL* 4.4 15.7 - - + -
97B LEU* 3.7 23.5 - - + +
98B HIS* 5.7 0.9 - - - -
258B LEU* 3.6 46.2 - - + +
259B ALA* 5.2 0.7 - - - -
261B ASN* 3.3 12.3 - - + +
262B SER 3.3 0.6 - - - -
263B SER* 1.4 78.0 - - - +
265B ILE* 1.3 66.7 + - + +
266B HIS 3.0 1.2 + - - -
267B VAL* 3.2 13.7 + - - +
268B TYR* 3.4 35.1 + + - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASN* 5.9 0.9 - - - +
259A ALA* 4.4 24.9 - - + +
259B ALA 5.3 7.9 - - - +
260B GLU* 5.4 2.5 - - - -
261B ASN 3.3 24.0 - - - +
262B SER* 3.4 11.0 + - - +
264B TYR* 1.3 81.1 - - + +
266B HIS* 1.3 63.5 + - - +
268B TYR* 3.1 8.2 + - + +
269B ARG* 3.0 32.8 + - - +
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Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS* 5.6 4.6 + - - -
262B SER 3.1 13.5 + - - +
263B SER* 2.9 15.5 + - - +
265B ILE* 1.3 75.9 - - - +
267B VAL* 1.3 61.3 + - - +
269B ARG* 4.2 25.6 - - + +
270B GLU* 2.9 50.5 + - - +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 3.4 36.4 - - + +
93B LYS* 4.2 23.6 - - + -
94B VAL* 4.1 9.6 - - + -
97B LEU* 4.3 12.1 - - + -
263B SER* 2.9 20.0 + - - +
264B TYR* 3.2 13.2 - - - +
266B HIS* 1.3 78.8 + - - +
268B TYR* 1.3 70.8 + - + +
270B GLU* 3.7 10.4 + - - +
271B LEU* 2.9 25.6 + - - +
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Residues in contact with TYR 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 4.7 3.1 + - - -
253A LYS* 3.6 17.8 + - - -
256A LEU* 3.7 22.5 + - + +
257A ASN* 3.3 55.0 - - + +
90B GLU* 2.6 33.9 + - + -
94B VAL* 3.5 12.2 - - + +
264B TYR* 3.4 43.6 + + - -
265B ILE* 3.1 8.2 + - + +
267B VAL* 1.3 87.9 - - + +
269B ARG* 1.3 58.8 + - - +
271B LEU* 3.7 10.3 - - + +
272B GLU* 2.9 29.3 + - - +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 3.0 26.0 + - + +
266B HIS* 3.1 25.3 + - + +
268B TYR* 1.3 73.4 - - - +
270B GLU* 1.3 64.3 + - - +
271B LEU 3.3 0.2 + - - -
272B GLU* 3.3 6.6 + - + +
273B GLN* 3.0 24.9 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 4.4 9.9 - - - +
93B LYS* 3.2 37.4 + - - +
266B HIS* 2.9 34.9 + - + +
267B VAL* 3.7 7.6 - - - +
269B ARG* 1.3 75.2 - - - +
271B LEU* 1.3 63.7 + - - +
273B GLN* 3.5 16.8 - - - +
274B ALA* 2.9 24.9 + - + +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A LYS* 3.5 32.1 - - + -
256A LEU* 5.2 2.0 - - + -
86B ALA* 3.7 27.8 - - + +
87B ILE* 3.8 20.2 - - + +
90B GLU* 3.9 30.5 - - + -
267B VAL 2.9 18.6 + - - +
268B TYR* 3.7 13.7 - - + +
269B ARG 3.2 0.4 - - - -
270B GLU* 1.3 75.4 - - - +
272B GLU* 1.3 64.2 + - - +
274B ALA* 3.2 3.8 + - - +
275B ILE* 3.0 37.2 + - + +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 4.0 14.0 - - + +
253A LYS* 3.2 32.6 + - + +
254A ARG* 5.2 4.2 + - - -
260A GLU* 5.6 0.2 - - - +
268B TYR 2.9 17.4 + - - +
269B ARG* 3.8 5.8 - - - +
270B GLU 3.3 0.2 - - - -
271B LEU* 1.3 77.1 - - - +
273B GLN* 1.3 56.5 + - - +
275B ILE* 3.4 5.4 + - - +
276B ARG* 2.9 66.2 + - - +
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Residues in contact with GLN 273 (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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269B ARG 3.0 16.7 + - - +
270B GLU* 3.5 17.4 - - - +
272B GLU* 1.3 72.9 - - - +
274B ALA* 1.3 67.3 + - - +
276B ARG* 4.0 4.8 - - - +
277B GLY* 3.1 20.3 + - - -
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Residues in contact with ALA 274 (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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82B ARG 5.3 1.1 - - - +
83B ALA* 4.3 8.0 - - - +
86B ALA* 3.7 26.0 - - + -
270B GLU* 2.9 14.4 + - + +
271B LEU* 3.5 7.9 - - - +
273B GLN* 1.3 78.0 - - - +
275B ILE* 1.3 65.6 + - - +
277B GLY* 3.1 14.1 + - - -
278B ALA 3.7 3.3 + - - -
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Residues in contact with ILE 275 (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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246A LYS* 3.5 18.1 - - + +
249A LEU* 3.5 35.2 - - + +
250A LEU* 3.6 35.0 - - + +
253A LYS* 4.0 13.0 - - + -
83B ALA* 3.8 25.7 - - + +
87B ILE* 4.9 4.0 - - + -
271B LEU* 3.0 40.1 + - + +
272B GLU 3.9 3.6 - - - +
274B ALA* 1.3 77.3 - - - +
276B ARG* 1.3 62.4 + - - +
278B ALA* 3.2 20.3 + - - +
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Residues in contact with ARG 276 (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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246A LYS* 3.1 26.1 + - - +
250A LEU* 4.4 26.5 - - + +
254A ARG* 4.6 10.9 - - - +
272B GLU* 2.9 55.3 + - + +
273B GLN* 4.0 5.6 - - - +
275B ILE* 1.3 73.0 - - - +
277B GLY* 1.3 64.3 + - - +
278B ALA 3.5 0.2 - - - +
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Residues in contact with GLY 277 (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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79B SER* 4.8 2.8 + - - -
82B ARG* 6.3 0.2 - - - -
273B GLN 3.1 14.3 + - - -
274B ALA* 3.1 6.8 + - - -
276B ARG* 1.3 76.6 - - - +
278B ALA* 1.3 59.3 + - - +
279B ASP* 3.7 9.5 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 2.8 35.9 + - + +
79B SER* 3.2 35.7 - - - +
80B LEU* 4.1 14.8 - - + -
83B ALA* 3.9 12.3 - - + -
274B ALA 3.7 3.0 + - - +
275B ILE 3.2 14.4 + - - +
276B ARG 3.1 1.9 - - - +
277B GLY* 1.3 75.3 - - - +
279B ASP* 1.3 59.4 + - - +
280B ALA 4.3 0.4 - - - -
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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