Contacts of the helix formed by residues 305 - 312 (chain B) in PDB entry 1HQC
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 305 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B GLY 2.5 31.3 + - - +
294B LEU* 2.5 22.8 + - - +
295B LEU* 4.6 3.0 - - - +
296B LYS* 5.4 10.5 - - - +
303B VAL* 4.0 1.9 + - - -
304B PRO* 1.3 78.1 - - - +
306B GLU* 1.3 74.6 + - - +
307B LEU* 3.3 12.1 + - + +
308B ALA* 3.0 32.2 + - - +
309B TYR* 3.5 5.4 + - - -
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Residues in contact with GLU 306 (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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305B THR* 1.3 75.7 + - - +
307B LEU* 1.3 55.4 + - - +
308B ALA 2.6 13.2 + - - -
309B TYR* 2.6 27.4 + - - +
310B ARG* 2.9 35.9 + - - +
316B PRO* 4.3 17.8 - - + +
317B PRO* 5.1 7.6 - - + +
318B VAL* 6.1 0.5 - - - +
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Residues in contact with LEU 307 (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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243B LEU* 5.3 6.5 - - + -
292B GLN* 3.5 27.1 - - - +
293B GLY* 4.0 4.9 - - - +
294B LEU* 3.7 11.0 - - + -
305B THR* 3.3 13.6 + - + +
306B GLU* 1.3 79.7 - - - +
308B ALA* 1.3 51.2 + - - +
310B ARG* 3.5 34.0 - - + +
311B HIS* 2.6 38.5 + - + +
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Residues in contact with ALA 308 (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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253B LEU* 4.2 17.3 - - + -
257B ILE* 4.0 7.0 - - + -
294B LEU* 3.6 29.6 - - - +
304B PRO* 3.8 15.9 - - + -
305B THR* 3.0 17.7 - - + +
306B GLU 2.6 4.4 + - - -
307B LEU* 1.3 69.6 - - - +
309B TYR* 1.3 68.2 + - - +
311B HIS* 2.7 14.4 + - - +
312B LEU* 2.8 16.2 + - - +
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Residues in contact with TYR 309 (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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257B ILE* 3.2 43.5 + - + -
261B GLY 3.1 33.1 + - - -
262B GLY* 3.6 1.4 + - - -
304B PRO* 3.7 22.2 - - + -
305B THR 3.7 11.9 - - - -
306B GLU* 2.6 14.1 + - - +
308B ALA* 1.3 77.6 - - - +
310B ARG* 1.3 60.9 + - - +
312B LEU 3.2 1.9 + - - -
313B GLY 3.1 4.7 + - - -
314B TYR* 2.8 41.6 + - + +
315B PRO* 4.2 1.8 - - + -
316B PRO* 4.3 9.0 - - + -
317B PRO* 3.5 48.0 - - + +
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Residues in contact with ARG 310 (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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306B GLU* 2.9 36.9 + - - +
307B LEU* 3.7 41.9 - - + +
309B TYR* 1.3 78.6 - - - +
311B HIS* 1.3 61.7 + - - +
313B GLY* 3.5 8.9 + - - -
314B TYR 4.4 8.1 - - - -
316B PRO* 4.1 19.9 - - + +
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Residues in contact with HIS 311 (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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241B ASP* 2.7 30.0 + - + +
242B GLU* 3.8 17.9 - - - -
243B LEU* 3.6 37.5 - - + +
245B LEU* 4.2 12.5 - - + +
250B ARG* 4.6 1.5 - - - -
253B LEU* 5.3 1.1 - - + -
294B LEU* 4.3 8.7 - - + -
307B LEU* 2.6 24.1 + - + +
308B ALA* 2.7 8.4 + - - +
310B ARG* 1.3 69.3 - - - +
312B LEU* 1.3 70.5 + - + +
313B GLY* 2.9 9.5 + - - -
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Residues in contact with LEU 312 (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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250B ARG* 3.5 34.1 - - + +
253B LEU* 3.5 17.9 - - + -
254B GLU* 3.4 42.4 - - + +
257B ILE* 3.7 15.3 - - + -
308B ALA 2.8 13.5 + - - +
311B HIS* 1.3 85.5 - - + +
313B GLY* 1.3 57.9 + - - +
314B TYR* 2.9 34.3 - - + -
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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