Contacts of the helix formed by residues 258 - 272 (chain H) in PDB entry 6BAA
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 ARG 258 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253H LEU 5.2 6.5 + - - +
254H PRO 4.5 0.9 - - - +
255H ILE* 3.5 44.8 + - - +
256H ALA 3.0 7.7 + - - -
257H MET* 1.3 77.3 - - - +
259H ALA* 1.3 58.8 + - - +
260H LEU* 3.6 15.7 - - + +
261H THR* 3.2 30.3 - - - +
262H ASN* 2.6 41.0 + - - +
1232H ASP* 4.7 14.7 + - - +
1235H ASN* 5.6 1.8 - - - -
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Residues in contact with ALA 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ARG* 1.3 72.1 - - - +
260H LEU* 1.3 50.8 + - - +
262H ASN* 4.6 1.6 - - - +
263H TYR* 2.8 39.8 + - - +
389H GLY* 3.9 19.1 - - - +
390H ALA* 4.2 1.5 - - - +
393H THR* 3.5 15.6 + - - +
1228H LEU* 3.4 23.3 - - + +
1231H THR* 4.2 13.7 - - + -
1232H ASP* 3.7 17.1 + - - +
1235H ASN* 5.2 4.3 - - - +
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Residues in contact with LEU 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ARG* 3.6 14.3 - - + +
259H ALA* 1.3 79.8 - - - +
261H THR* 1.3 65.5 + - - +
263H TYR* 3.6 8.8 - - + +
264H GLN* 2.8 37.6 + - + +
393H THR* 5.6 1.1 - - - -
1228H LEU* 3.9 29.2 - - + +
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Residues in contact with THR 261 (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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255H ILE 3.6 4.4 + - - +
256H ALA* 3.8 25.1 - - + +
258H ARG* 3.2 33.0 - - - +
260H LEU* 1.3 80.1 - - - +
262H ASN* 1.3 61.6 + - - +
264H GLN* 3.1 7.5 + - + +
265H ARG* 3.0 41.0 + - + +
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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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256H ALA 3.6 10.5 - - - +
258H ARG 2.6 32.2 + - - +
259H ALA* 4.3 1.4 - - - +
261H THR* 1.3 76.1 - - - +
263H TYR* 1.3 58.4 + - - +
265H ARG* 2.5 36.6 + - - +
266H LEU* 2.9 28.6 + - - +
295H PHE* 4.5 5.9 - - + -
386H ASN* 2.5 60.7 + - + +
389H GLY* 5.9 0.2 - - - -
390H ALA* 3.6 7.4 - - + +
1235H ASN* 5.5 2.0 - - - +
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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
----------------------------------------------------------
259H ALA 2.8 23.6 + - - +
260H LEU* 3.6 6.7 - - + +
262H ASN* 1.3 77.9 - - - +
264H GLN* 1.3 59.8 + - + +
266H LEU* 3.3 10.7 + - + +
267H CYS* 2.8 47.3 + - - -
390H ALA* 3.4 26.1 - - - +
393H THR* 3.6 14.6 - - + -
394H LYS* 3.4 46.1 + - + +
397H ASN* 2.9 35.2 + - - +
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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
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260H LEU* 2.8 27.2 + - + +
261H THR* 3.1 10.7 + - + +
263H TYR* 1.3 78.1 - - + +
265H ARG* 1.3 61.0 + - + +
267H CYS* 3.1 14.4 + - - +
268H VAL* 2.9 35.5 + - + +
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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
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256H ALA 5.0 1.0 + - - -
261H THR* 3.0 29.2 + - + +
262H ASN* 2.5 36.4 + - - +
264H GLN* 1.3 74.4 - - + +
266H LEU* 1.3 60.8 + - - +
268H VAL* 3.2 13.6 + - + +
269H ALA* 2.9 27.0 + - - +
294H ALA* 3.1 34.8 + - + +
295H PHE* 3.7 20.3 - - + -
386H ASN* 4.9 2.8 - - - +
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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
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262H ASN 2.9 17.9 + - - +
263H TYR* 3.4 31.0 - - + +
264H GLN 3.2 0.2 - - - -
265H ARG* 1.3 77.0 - - - +
267H CYS* 1.3 59.2 + - - +
269H ALA* 3.2 8.6 + - + +
270H PHE* 2.9 51.5 + - + -
290H ALA* 6.2 0.9 - - + -
291H LEU* 4.6 15.3 - - + -
294H ALA* 4.5 8.2 - - + +
295H PHE* 5.2 4.3 - - + -
387H LEU* 5.0 3.6 - - + -
390H ALA* 3.9 19.7 - - + -
391H ILE* 4.4 19.3 - - + -
394H LYS* 4.0 17.7 - - + -
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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
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263H TYR* 2.8 57.9 + - - -
264H GLN* 3.4 19.7 - - - +
266H LEU* 1.3 75.5 - - - +
268H VAL* 1.3 61.0 + - - +
270H PHE* 3.3 7.6 + - - +
271H ASP* 2.9 38.0 + - - +
394H LYS* 5.0 7.0 - - - +
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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* 2.9 29.8 + - + +
265H ARG* 3.4 14.8 - - + +
267H CYS* 1.3 75.6 - - - +
269H ALA* 1.3 58.1 + - - +
271H ASP* 3.2 14.0 + - + +
272H ALA* 3.0 27.7 + - + +
293H HIS* 5.3 9.0 - - + +
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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 2.9 13.2 + - - +
266H LEU* 3.2 9.8 + - + +
268H VAL* 1.3 74.2 - - - +
270H PHE* 1.3 67.0 + - - +
272H ALA* 3.2 18.0 + - - +
290H ALA* 3.0 45.9 - - + +
293H HIS* 4.2 15.9 - - + -
294H ALA* 3.9 11.0 - - + +
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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
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266H LEU* 2.9 46.7 + - + +
267H CYS* 3.6 9.2 - - - +
269H ALA* 1.3 78.4 - - - +
271H ASP* 1.3 68.3 + - - +
272H ALA 3.2 5.5 + - - -
286H ALA* 5.9 2.7 - - + -
287H ILE* 3.5 42.6 - - + -
290H ALA* 4.2 16.2 - - + -
291H LEU* 6.2 1.8 - - + -
394H LYS* 4.3 29.4 - - + +
614H LEU* 6.3 2.7 - - + -
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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* 2.9 25.8 + - - +
268H VAL* 3.4 14.8 - - + +
270H PHE* 1.3 79.5 - - - +
272H ALA* 1.3 60.8 + - - +
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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* 3.0 13.1 + - + +
269H ALA 3.5 14.6 - - - +
270H PHE 3.1 8.2 - - - -
271H ASP* 1.3 80.9 - - - +
293H HIS* 4.4 21.8 - - + +
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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