Contacts of the helix formed by residues 294 - 299 (chain A) in PDB entry 2QMQ
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASP* 4.1 4.4 + - - -
73A LEU* 3.8 13.5 - - + +
145A VAL* 3.7 9.0 - - - +
170A ASN* 3.6 11.3 - - - +
201A LEU* 3.0 47.9 + - + +
202A PHE* 3.5 26.6 - - + -
206A GLU* 5.0 0.4 + - - -
291A SER 4.3 2.1 + - - -
292A GLY 3.4 0.6 - - - -
293A GLY* 1.3 83.9 + - - +
295A PRO* 1.3 61.2 - - - +
296A GLN* 2.9 30.2 + - - +
297A LEU* 2.8 40.5 + - + +
298A THR* 3.2 14.6 + - + +
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Residues in contact with PRO 295 (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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169A ILE* 4.0 13.2 - - + -
170A ASN* 4.4 1.8 - - - +
260A VAL* 4.2 17.5 - - + -
261A VAL* 4.4 1.1 - - - -
262A GLY 4.1 11.7 - - - +
288A MET* 3.7 25.1 - - - -
291A SER* 3.8 18.4 - - - +
292A GLY 4.0 2.5 - - - +
293A GLY 3.3 9.4 - - - +
294A GLN* 1.3 89.3 - - - +
296A GLN* 1.3 61.6 + - - +
297A LEU 3.1 0.4 - - - -
298A THR* 3.6 9.6 - - - +
299A GLN* 2.9 34.7 + - - +
303A LEU* 4.5 3.4 - - + +
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Residues in contact with GLN 296 (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 CYS* 3.2 40.2 + - - +
79A PHE* 4.8 4.7 - - + -
81A PRO* 4.2 1.4 - - - +
82A LEU* 3.7 36.0 + - + +
145A VAL* 4.0 14.4 - - + +
169A ILE* 4.2 15.1 - - + +
294A GLN* 2.9 38.3 + - - +
295A PRO* 1.3 79.7 - - - +
297A LEU* 1.3 70.8 + - - +
299A GLN 4.8 0.4 - - - -
300A PRO* 4.4 7.2 - - - +
303A LEU* 3.7 25.5 - - + +
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Residues in contact with LEU 297 (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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73A LEU* 5.4 2.0 - - + -
77A SER 3.5 10.5 - - - +
78A CYS 3.8 13.0 - - - +
81A PRO* 3.6 28.9 - - + +
202A PHE* 4.2 9.0 - - + -
213A LEU* 4.2 20.3 - - + +
217A TYR* 3.5 46.9 - - + +
294A GLN* 2.8 37.7 + - + +
296A GLN* 1.3 87.3 - - - +
298A THR* 1.3 58.6 + - - +
299A GLN 3.8 0.2 - - - -
300A PRO* 4.1 7.0 - - - +
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Residues in contact with THR 298 (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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202A PHE* 5.9 0.2 - - + -
206A GLU* 4.5 7.9 - - - +
213A LEU* 3.6 28.5 - - + -
290A ASP 4.9 2.2 - - - -
291A SER* 2.6 39.1 + - - +
294A GLN* 3.2 10.5 + - + +
295A PRO* 3.6 2.3 - - - +
297A LEU* 1.3 76.1 - - - +
299A GLN* 1.3 71.0 + - - +
300A PRO* 3.2 10.2 - - - +
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Residues in contact with GLN 299 (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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288A MET* 3.3 21.7 - - + +
290A ASP* 3.1 30.1 + - - +
291A SER* 3.8 15.5 - - - +
295A PRO 2.9 13.4 + - - +
298A THR* 1.3 93.9 + - - +
300A PRO* 1.3 63.7 - - - +
301A GLY 3.2 3.5 + - - +
302A LYS* 3.3 31.3 + - + +
303A LEU* 3.0 21.1 + - - +
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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