Contacts of the helix formed by residues 264 - 273 (chain B) in PDB entry 1HQR
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 GLN 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B TYR* 5.0 4.7 - - + +
261B TRP* 2.9 24.0 + - + +
262B ASN 3.2 0.9 - - - -
263B SER* 1.3 80.7 + - - +
265B LYS* 1.3 54.9 + - - +
266B ASP* 2.5 22.3 + - + +
267B PHE* 2.9 24.4 + - + +
268B LEU* 3.4 6.3 + - - -
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Residues in contact with LYS 265 (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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262B ASN 4.4 3.9 + - - -
263B SER 3.5 5.7 + - - -
264B GLN* 1.3 71.9 - - - +
266B ASP* 1.3 67.5 + - - +
268B LEU* 3.1 17.2 + - - +
269B GLU* 3.2 12.2 + - + +
272B ARG* 5.1 15.3 + - - +
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Residues in contact with ASP 266 (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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264B GLN* 2.5 11.0 + - + +
265B LYS* 1.3 73.3 - - - +
267B PHE* 1.3 58.9 + - - +
268B LEU 2.5 0.3 + - - -
269B GLU* 2.5 41.3 + - - +
270B ASP* 3.5 16.3 + - - +
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Residues in contact with PHE 267 (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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247B TYR* 3.2 31.9 - + - -
261B TRP* 3.3 52.9 - + + -
264B GLN* 2.9 11.7 + - + +
266B ASP* 1.3 82.6 - - + +
268B LEU* 1.3 61.0 + - + +
269B GLU 3.3 0.2 - - - -
270B ASP* 3.7 13.1 + - + +
271B ARG* 3.0 70.1 + - + +
415C PRO* 3.5 24.7 - - + -
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Residues in contact with LEU 268 (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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240B PHE* 3.6 28.7 - - + -
245B GLY 3.7 5.8 - - - +
246B GLU* 3.8 13.5 - - + -
247B TYR* 4.1 10.5 - - + -
261B TRP 5.1 2.0 - - - +
262B ASN* 3.6 42.6 - - + +
264B GLN 3.4 4.1 + - - +
265B LYS* 3.3 16.2 - - - +
266B ASP 2.5 6.3 + - - -
267B PHE* 1.3 77.2 - - + +
269B GLU* 1.3 58.0 + - - -
271B ARG* 3.8 1.9 + - - +
272B ARG* 2.8 60.7 + - - +
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Residues in contact with GLU 269 (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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265B LYS* 3.2 7.9 + - + +
266B ASP* 2.5 19.6 + - - +
268B LEU* 1.3 70.8 - - - +
270B ASP* 1.3 67.0 + - - +
271B ARG 3.1 0.4 - - - -
272B ARG* 3.1 15.4 + - - +
273B ALA* 3.0 26.0 + - - +
617D ASN* 5.5 0.4 - - - -
618D ASN* 5.0 14.4 - - - +
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Residues in contact with ASP 270 (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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266B ASP* 3.5 18.4 + - - +
267B PHE* 3.8 16.0 - - + +
268B LEU 3.4 0.2 - - - -
269B GLU* 1.3 83.0 - - - +
271B ARG* 1.3 66.9 + - - +
273B ALA* 3.6 8.9 + - - +
274B ALA* 3.7 11.4 + - - +
277B THR* 5.0 1.7 + - - -
412C ILE* 5.5 1.6 - - - +
615D ASN* 3.5 31.3 + - - +
617D ASN* 3.9 17.9 - - - +
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Residues in contact with ARG 271 (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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213B TYR* 3.7 17.8 + - - -
226B PHE* 4.0 23.0 - - + +
228B HIS* 3.9 1.6 + - - +
240B PHE* 3.3 34.4 - - + -
247B TYR* 2.5 37.1 + - + +
267B PHE* 3.0 50.2 + - + +
268B LEU 4.2 1.3 - - - +
269B GLU 3.1 0.6 - - - -
270B ASP* 1.3 80.9 - - - +
272B ARG* 1.3 67.4 + - - +
273B ALA 3.1 0.8 + - - -
274B ALA* 3.3 16.8 + - - +
275B VAL* 4.8 1.0 + - - +
412C ILE* 3.6 23.6 - - - +
413C VAL 2.8 28.9 + - - -
414C THR* 4.4 1.0 - - - +
415C PRO* 3.4 7.7 - - - +
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Residues in contact with ARG 272 (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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240B PHE* 4.4 7.4 - - + -
242B SER* 5.8 4.0 - - - +
245B GLY* 2.9 33.3 + - - +
246B GLU* 5.0 2.4 - - - +
265B LYS* 5.1 17.0 + - - +
268B LEU* 2.8 51.4 + - - +
269B GLU* 3.1 14.3 + - - +
271B ARG* 1.3 80.5 - - - +
273B ALA* 1.3 56.9 + - - +
274B ALA 3.6 0.7 + - - -
275B VAL* 4.2 18.2 + - - +
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Residues in contact with ALA 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 GLU 3.0 14.6 + - - +
270B ASP 4.0 4.0 - - - +
271B ARG 3.1 0.4 - - - -
272B ARG* 1.3 75.8 - - + +
274B ALA* 1.3 58.6 + - - +
275B VAL* 3.3 3.6 - - - -
276B ASP* 3.2 5.5 + - - +
277B THR* 2.8 33.2 + - - +
603D LEU* 3.6 35.4 - - + -
617D ASN* 3.7 14.1 - - - +
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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