Contacts of the helix formed by residues 307 - 316 (chain A) in PDB entry 1QO0
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 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.0 1.6 - - - -
305A ASN* 3.1 38.1 + - - +
306A TRP* 1.3 75.7 - - - +
308A VAL* 1.3 67.8 + - - +
309A GLU* 4.6 3.1 - - + +
310A ASP* 3.2 15.3 + - - +
311A VAL* 3.0 22.0 + - - +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ARG* 3.7 34.1 - - + +
78A PHE* 3.7 19.9 - - + -
99A ASP 3.7 26.5 - - - +
100A ALA* 4.2 3.8 - - - +
101A LEU* 4.1 13.9 - - + +
116A ASN* 5.9 0.4 - - - +
306A TRP 3.9 0.4 + - - -
307A ARG* 1.3 71.1 - - - +
309A GLU* 1.3 55.8 + - - +
312A GLN* 2.7 58.8 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ARG* 3.3 3.2 - - + +
308A VAL* 1.3 77.7 - - - +
310A ASP* 1.3 65.5 + - - +
312A GLN* 4.2 4.5 - - - +
313A ARG* 3.3 36.4 + - - +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA* 3.7 11.0 - - + +
305A ASN* 2.5 41.7 + - - +
307A ARG* 3.2 19.6 + - - +
309A GLU* 1.3 77.6 - - - +
311A VAL* 1.3 64.3 + - - +
313A ARG* 3.2 37.1 + - - +
314A HIS* 3.1 25.3 + - - -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.9 28.9 - - + -
296A LEU* 3.8 32.1 - - + +
299A ALA* 3.5 10.9 - - + +
300A ALA* 3.8 17.7 - - + +
303A ALA* 4.1 6.1 - - + -
305A ASN* 3.6 24.9 - - - +
306A TRP* 4.2 3.4 - - + -
307A ARG 3.0 22.2 + - - +
308A VAL 4.0 1.3 - - - +
310A ASP* 1.3 72.2 - - - +
312A GLN* 1.3 68.8 + - - +
313A ARG 3.3 0.3 + - - -
314A HIS 3.3 2.8 + - - -
315A LEU* 3.3 16.9 + - + +
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Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.8 27.6 - - + +
115A PRO 3.0 21.9 + - - +
116A ASN* 5.5 1.8 - - - +
118A VAL* 5.9 0.2 - - + -
308A VAL* 2.7 42.9 + - - +
309A GLU* 4.2 4.5 - - - +
311A VAL* 1.3 74.9 - - - +
313A ARG* 1.3 62.2 + - - +
315A LEU* 3.2 18.4 + - + +
316A TYR* 2.5 53.4 + - + +
334A ASN* 4.4 0.5 + - - -
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA* 5.6 0.4 - - - +
309A GLU* 3.3 36.0 + - - +
310A ASP* 3.2 45.1 + - - +
311A VAL 3.3 0.2 - - - -
312A GLN* 1.3 78.6 - - - +
314A HIS* 1.3 77.8 + - + +
315A LEU 3.3 0.5 + - - -
316A TYR* 3.5 14.1 + - - +
317A ASP* 4.1 5.5 - - - +
331A ARG* 3.5 24.1 + - - +
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ALA* 3.8 17.5 - - + +
302A ALA* 3.5 29.0 + - + +
303A ALA* 3.9 18.2 - - - -
310A ASP 3.1 18.3 + - - +
311A VAL 3.3 9.4 + - - +
313A ARG* 1.3 97.1 - - + +
315A LEU* 1.3 59.7 + - - +
316A TYR 3.4 0.7 - - - -
317A ASP* 3.9 11.2 + - + +
318A ILE* 3.4 27.9 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.4 1.3 - - + -
103A CYS* 5.6 1.8 - - - -
118A VAL* 4.6 18.6 - - + -
292A GLN 5.3 1.1 - - - +
295A LEU* 3.6 48.2 - - + +
296A LEU* 4.0 31.6 - - + +
299A ALA* 3.6 9.0 - - + -
311A VAL 3.3 10.2 + - - +
312A GLN* 3.2 17.5 + - + +
314A HIS* 1.3 75.4 - - - +
316A TYR* 1.3 88.4 + - + +
317A ASP 3.3 1.6 + - - -
318A ILE 3.7 9.3 + - - +
329A VAL* 4.3 14.2 + - + +
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Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 5.1 2.8 - - + +
312A GLN* 2.5 64.2 + - + +
313A ARG* 3.5 9.1 + - - -
314A HIS 3.4 0.2 - - - -
315A LEU* 1.3 84.5 - - + +
317A ASP* 1.3 58.4 + - - +
318A ILE 3.7 1.0 - - - +
319A ASP* 5.6 0.5 - - - +
328A ARG* 5.4 9.2 + - - +
329A VAL* 3.5 37.9 + - + +
331A ARG* 3.6 70.9 + - + +
334A ASN* 2.6 30.1 + - - -
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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