Contacts of the helix formed by residues 261 - 277 (chain H) in PDB entry 5TWV
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 THR 261 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221H PHE* 5.6 4.1 + - - +
259H ALA 3.6 0.4 - - - -
260H LEU* 1.3 76.6 - - - +
262H ASN* 1.3 57.4 + - - +
263H TYR 3.2 2.0 - - - +
264H GLN* 3.2 14.6 + - - -
265H ARG* 2.9 28.8 + - - +
1236H ILE* 4.0 19.2 - - - +
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Residues in contact with ASN 262 (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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259H ALA* 3.2 29.5 + - + +
260H LEU 2.8 1.6 + - - -
261H THR* 1.3 78.0 - - - +
263H TYR* 1.3 59.5 + - - +
264H GLN 3.2 2.8 + - - -
265H ARG* 3.8 12.4 + - - +
266H LEU* 3.8 13.9 + - - +
1232H ASP* 5.1 14.4 - - + -
1236H ILE* 4.9 2.2 - - + +
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Residues in contact with TYR 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H LEU* 6.0 5.2 - - + -
260H LEU 3.7 7.7 + - - +
261H THR 3.2 0.4 - - - -
262H ASN* 1.3 79.3 - - - +
264H GLN* 1.3 58.9 + - - +
266H LEU* 4.5 6.6 - - - +
267H CYS* 4.4 11.3 + - - +
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Residues in contact with GLN 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H THR* 3.2 18.7 + - - +
262H ASN 3.2 0.4 - - - -
263H TYR* 1.3 81.4 - - - +
265H ARG* 1.3 63.3 + - - +
266H LEU 3.3 1.3 - - - -
267H CYS* 3.7 8.5 + - - +
268H VAL* 3.3 25.1 + - - +
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Residues in contact with ARG 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H THR 2.9 15.9 + - - +
262H ASN* 3.8 9.2 + - - +
264H GLN* 1.3 77.8 - - - +
266H LEU* 1.3 62.5 + - - +
268H VAL* 3.2 10.7 + - - +
269H ALA* 3.1 19.8 + - - +
386H ASN* 5.8 4.9 - - - +
389H GLY* 6.0 2.4 - - - -
390H ALA* 5.5 1.7 + - - +
1228H LEU* 5.4 12.1 - - + -
1232H ASP* 5.6 9.9 - - + -
1235H ASN* 5.8 6.3 - - + -
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Residues in contact with LEU 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H ASN 3.8 13.2 + - - +
263H TYR* 4.7 7.0 - - - +
264H GLN 3.3 0.2 - - - -
265H ARG* 1.3 77.2 - - - +
267H CYS* 1.3 64.2 + - - +
269H ALA* 3.2 9.0 + - - +
270H PHE* 3.0 23.4 + - - +
1228H LEU* 5.3 16.3 - - + +
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Residues in contact with CYS 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H TYR 4.4 9.2 + - - +
264H GLN* 3.7 14.6 + - - +
265H ARG 3.3 0.8 - - - -
266H LEU* 1.3 76.8 - - - +
268H VAL* 1.3 52.6 + - + +
270H PHE* 3.1 8.5 + - - +
271H ASP* 2.5 36.9 + - - +
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Residues in contact with VAL 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H GLN 3.3 16.8 - - - +
265H ARG* 3.2 9.7 + - - +
267H CYS* 1.3 75.0 - - + +
269H ALA* 1.3 67.8 + - - +
271H ASP* 3.5 8.8 - - + +
272H ALA* 2.9 23.0 + - + +
295H PHE* 5.3 9.9 - - + -
386H ASN* 3.3 50.3 - - + +
390H ALA* 3.6 6.7 - - + -
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Residues in contact with ALA 269 (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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265H ARG 3.1 12.7 + - - +
266H LEU* 3.2 10.7 + - - +
268H VAL* 1.3 77.3 - - - +
270H PHE* 1.3 62.6 + - - +
272H ALA* 3.1 15.5 + - - +
273H GLN* 3.4 7.8 + - - +
389H GLY 5.7 0.2 - - - -
390H ALA* 3.8 15.1 - - - +
393H THR* 4.1 25.6 - - - -
1228H LEU* 5.9 4.3 - - + -
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Residues in contact with PHE 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H LEU 3.0 13.5 + - - +
267H CYS* 3.4 10.8 - - - +
269H ALA* 1.3 76.9 - - - +
271H ASP* 1.3 60.1 + - - +
273H GLN* 3.3 16.8 + - - +
274H ALA* 3.3 12.1 + - - +
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Residues in contact with ASP 271 (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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267H CYS 2.5 20.8 + - - +
268H VAL* 3.1 11.9 + - + +
270H PHE* 1.3 73.3 - - - +
272H ALA* 1.3 63.0 + - - +
274H ALA* 3.2 9.4 + - - +
275H ARG* 3.0 23.8 + - - +
294H ALA* 4.5 15.7 - - + +
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Residues in contact with ALA 272 (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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268H VAL* 2.9 12.1 + - + +
269H ALA* 3.1 11.0 + - - +
271H ASP* 1.3 77.4 - - - +
273H GLN* 1.3 62.1 + - - +
275H ARG* 3.3 8.0 + - - +
276H LYS* 3.0 23.8 + - - +
294H ALA* 4.5 9.2 - - + +
390H ALA* 4.3 18.2 - - + +
391H ILE* 6.2 0.4 - - - -
394H LYS* 5.8 6.7 - - + -
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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 ALA 3.4 6.9 + - - +
270H PHE* 3.3 12.0 + - - +
271H ASP 3.2 0.4 - - - -
272H ALA* 1.3 78.4 - - - +
274H ALA* 1.3 62.9 + - - +
276H LYS* 3.3 8.4 + - - +
277H ASP* 3.0 22.0 + - - +
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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
----------------------------------------------------------
270H PHE 3.3 8.5 + - - +
271H ASP* 3.2 12.9 + - - +
273H GLN* 1.3 80.2 - - - +
275H ARG* 1.3 60.7 + - - +
277H ASP* 3.3 23.7 + - - +
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Residues in contact with ARG 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H ASP 3.0 8.9 + - - +
272H ALA 3.6 6.7 - - - +
273H GLN 3.3 0.2 - - - -
274H ALA* 1.3 76.9 - - - +
276H LYS* 1.3 62.8 + - - +
277H ASP 3.4 3.8 + - - +
278H THR* 4.6 4.7 + - - -
290H ALA* 3.4 40.0 - - + +
293H HIS* 4.3 16.8 - - + -
294H ALA* 3.4 26.0 - - + +
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Residues in contact with LYS 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ALA 3.0 13.7 + - - +
273H GLN* 3.5 11.2 - - - +
275H ARG* 1.3 78.0 - - - +
277H ASP* 1.3 49.3 + - - +
278H THR* 2.6 24.9 + - - -
290H ALA* 4.1 10.9 - - + +
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Residues in contact with ASP 277 (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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273H GLN 3.0 12.4 + - - +
274H ALA* 3.4 19.5 - - - +
275H ARG 3.2 2.8 - - - +
276H LYS* 1.3 71.5 - - - +
278H THR* 1.3 60.0 + - - +
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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