Contacts of the helix formed by residues 262 - 278 (chain H) 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 SER 262 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260H GLU 3.7 3.8 + - - -
261H ASN* 1.3 76.7 - - - +
263H SER* 1.3 61.7 + - - -
264H TYR 3.2 1.6 + - - -
265H ILE* 3.9 10.0 + - - +
266H HIS* 4.1 7.1 + - - +
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Residues in contact with SER 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H LEU* 4.7 11.2 - - - -
261H ASN* 2.6 25.7 + - - +
262H SER* 1.3 71.8 - - - +
264H TYR* 1.3 63.1 + - - -
265H ILE 3.4 0.4 - - - -
266H HIS* 3.1 19.4 + - - +
267H VAL* 3.2 17.5 + - - +
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Residues in contact with TYR 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G LEU 5.3 0.2 + - - -
258G LEU* 3.4 27.8 + - - +
259G ALA* 3.5 32.5 + - + -
264G TYR* 4.1 13.7 - + - -
94H VAL* 4.2 14.9 - - + +
97H LEU* 3.7 23.3 - - + -
98H HIS* 5.8 0.5 + - - -
258H LEU* 3.5 60.0 - - + +
259H ALA* 4.2 4.9 - - - -
261H ASN* 3.2 6.8 + - + +
262H SER 3.2 1.4 + - - -
263H SER* 1.3 75.6 - - - +
265H ILE* 1.3 70.3 + - + +
266H HIS 3.1 0.5 + - - -
267H VAL* 3.2 13.4 + - + +
268H TYR* 3.5 36.6 + + - -
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Residues in contact with ILE 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G ALA* 3.6 31.2 - - + +
260G GLU* 3.9 23.3 - - + +
259H ALA* 6.0 3.4 - - - +
261H ASN 4.5 1.9 + - - +
262H SER 3.9 7.2 + - - +
264H TYR* 1.3 77.2 - - + +
266H HIS* 1.3 58.1 + - - +
268H TYR* 2.9 23.0 + - - +
269H ARG* 3.1 22.0 + - - -
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Residues in contact with HIS 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H SER 4.1 4.2 + - - +
263H SER* 3.1 20.0 + - - +
264H TYR 3.1 0.6 - - - -
265H ILE* 1.3 81.0 - - - +
267H VAL* 1.3 62.0 + - - +
269H ARG* 4.3 17.1 - - + +
270H GLU* 3.0 44.5 + - + +
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Residues in contact with VAL 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H GLU* 4.1 17.8 - - + +
93H LYS* 4.0 31.0 - - + -
94H VAL* 4.4 7.9 - - + -
97H LEU* 4.7 11.4 - - + -
263H SER* 3.2 17.0 + - - +
264H TYR* 3.2 10.7 + - + +
265H ILE 3.1 0.4 + - - -
266H HIS* 1.3 76.3 - - - +
268H TYR* 1.3 90.3 + - + +
270H GLU* 3.7 11.0 - - - +
271H LEU* 3.1 26.5 + - - +
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Residues in contact with TYR 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ARG* 5.0 2.3 + - - -
253G LYS* 4.0 16.6 - - + +
256G LEU* 3.3 25.5 + - + +
257G ASN* 3.5 55.4 - - + +
258G LEU 4.8 0.4 - - - -
259G ALA* 4.0 1.3 - - + -
260G GLU* 4.0 3.4 - - - +
90H GLU* 2.9 29.0 + - - -
94H VAL* 3.8 9.3 - - + +
264H TYR* 3.5 34.4 + + - -
265H ILE 2.9 7.2 + - - +
267H VAL* 1.3 96.8 - - + +
269H ARG* 1.3 66.6 + - - +
271H LEU* 3.5 9.4 + - + +
272H GLU* 3.0 28.1 + - - +
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Residues in contact with ARG 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G LYS* 3.6 12.9 - - - +
257G ASN* 4.3 0.2 + - - -
260G GLU* 2.8 38.7 + - - -
265H ILE* 3.1 21.2 + - - +
266H HIS* 3.8 21.3 - - + +
268H TYR* 1.3 86.6 + - - +
270H GLU* 1.3 58.5 + - - +
272H GLU* 3.2 33.4 + - - +
273H GLN* 2.9 34.0 + - - +
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Residues in contact with GLU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H THR* 4.7 9.1 - - - +
93H LYS* 3.2 34.5 - - - +
266H HIS* 3.0 32.9 + - + +
267H VAL* 3.7 7.6 - - - +
269H ARG* 1.3 75.9 - - - +
271H LEU* 1.3 59.5 + - - +
273H GLN* 3.6 10.2 + - - +
274H ALA* 3.0 28.4 + - - +
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Residues in contact with LEU 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G LYS* 3.4 31.2 - - + -
256G LEU* 5.1 2.9 - - + -
86H ALA* 3.7 33.0 - - + +
87H ILE* 4.2 10.5 - - + -
90H GLU* 4.0 24.7 - - + -
267H VAL 3.1 18.3 + - - +
268H TYR* 3.7 14.1 - - + +
269H ARG 3.3 0.2 - - - -
270H GLU* 1.3 74.4 - - - +
272H GLU* 1.3 59.8 + - - +
274H ALA* 3.1 5.0 + - - +
275H ILE* 2.8 49.9 + - + +
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Residues in contact with GLU 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250G LEU* 4.5 7.0 - - + -
253G LYS* 2.8 44.4 + - + +
268H TYR 3.0 15.1 + - - +
269H ARG* 3.6 26.3 + - - +
271H LEU* 1.3 75.6 - - - +
273H GLN* 1.3 53.7 + - - +
275H ILE* 3.2 5.1 + - - +
276H ARG* 2.6 82.3 + - - +
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Residues in contact with GLN 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269H ARG* 2.9 18.2 + - - +
270H GLU* 3.7 10.9 - - - +
272H GLU* 1.3 76.7 - - - +
274H ALA* 1.3 64.7 + - - +
276H ARG* 2.9 8.3 + - - +
277H GLY* 2.9 23.7 + - - -
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Residues in contact with ALA 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ARG 5.3 0.9 - - - +
83H ALA* 3.8 13.1 - - - +
86H ALA* 3.7 24.7 - - + -
270H GLU 3.0 16.0 + - - +
271H LEU* 3.4 4.0 - - - +
273H GLN* 1.3 78.3 - - - +
275H ILE* 1.3 63.8 + - - +
277H GLY* 3.8 1.8 + - - -
278H ALA 3.7 10.6 + - - -
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Residues in contact with ILE 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G LYS* 3.6 17.1 - - + +
249G LEU* 3.6 48.5 - - + +
250G LEU* 3.4 29.8 - - + -
253G LYS* 4.2 8.1 - - + -
83H ALA* 4.0 18.6 - - + +
87H ILE* 4.8 4.3 - - + -
271H LEU* 2.8 47.0 + - + +
272H GLU 3.9 0.2 - - - +
273H GLN 3.0 0.2 + - - -
274H ALA* 1.3 74.6 - - - +
276H ARG* 1.3 64.7 + - - +
277H GLY 3.1 0.9 + - - -
278H ALA* 3.1 17.7 + - + +
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Residues in contact with ARG 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G LYS* 3.1 28.9 + - - +
250G LEU* 4.0 32.0 - - + +
272H GLU* 2.6 53.6 + - - +
273H GLN* 2.9 5.3 + - - +
275H ILE* 1.3 71.2 - - - +
277H GLY* 1.3 59.4 + - - +
278H ALA 3.5 0.2 - - - +
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Residues in contact with GLY 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H SER* 5.0 2.4 - - - -
273H GLN 2.9 14.5 + - - -
274H ALA* 4.2 2.5 - - - -
275H ILE 3.1 0.4 - - - -
276H ARG* 1.3 75.9 - - - +
278H ALA* 1.3 63.9 + - - +
279H ASP* 3.5 10.6 + - - +
282H GLU* 5.2 1.6 - - - +
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Residues in contact with ALA 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246G LYS* 2.9 33.6 + - + +
79H SER* 3.7 18.6 - - - +
80H LEU* 4.0 17.7 - - + -
83H ALA* 3.5 26.2 - - + -
274H ALA 3.7 4.8 + - - +
275H ILE* 3.1 13.8 + - + +
276H ARG 3.5 0.2 - - - +
277H GLY* 1.3 76.1 - - - +
279H ASP* 1.3 58.2 + - - +
280H ALA 4.4 0.2 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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