Contacts of the helix formed by residues 246 - 253 (chain A) in PDB entry 2Q5I
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ARG* 3.7 28.5 - - - +
245A GLU* 1.3 70.8 - - - +
247A ALA* 1.3 63.6 + - - +
248A GLN 3.2 3.7 + - - -
249A GLY 3.3 6.0 + - - +
250A ILE* 3.6 4.9 + - - +
271A GLN* 2.8 50.5 + - + +
273A GLY 4.5 11.2 - - - +
275A SER* 3.7 16.4 - - - +
294A MET* 4.8 5.2 - - + -
296A GLU* 2.5 41.7 + - - +
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Residues in contact with ALA 247 (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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245A GLU* 3.6 20.0 - - - +
246A THR* 1.3 77.0 - - - +
248A GLN* 1.3 62.3 + - - +
250A ILE* 3.1 10.1 + - - +
251A PHE* 3.0 33.0 + - + -
296A GLU* 3.2 13.1 + - - +
298A GLU* 3.4 34.1 - - - +
522A GLU* 4.9 2.0 - - - +
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Residues in contact with GLN 248 (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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134A VAL* 4.9 12.6 - - + -
135A LEU* 4.7 9.9 - - + -
138A SER* 3.5 21.3 - - - +
140A HIS* 3.9 7.1 - - + -
245A GLU* 2.9 35.2 + - + +
246A THR 3.2 1.0 - - - -
247A ALA* 1.3 76.4 - - - +
249A GLY* 1.3 57.7 + - - +
251A PHE* 3.2 10.1 + - - +
252A LEU* 2.8 35.5 + - + +
414A ASP* 3.3 30.8 + - - +
418A HIS* 2.6 36.0 + - + +
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Residues in contact with GLY 249 (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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126A CYS* 3.8 24.0 - - - -
245A GLU 5.5 0.4 + - - -
246A THR* 3.3 8.8 + - - +
247A ALA 3.2 1.0 - - - -
248A GLN* 1.3 76.9 - - - +
250A ILE* 1.3 62.2 + - - +
252A LEU* 3.4 8.7 + - - +
253A ASN* 2.6 35.0 + - - -
271A GLN* 3.9 1.6 - - - -
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Residues in contact with ILE 250 (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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124A ILE* 4.1 13.9 - - + -
246A THR* 3.6 8.6 + - - +
247A ALA* 3.1 8.8 + - - +
249A GLY* 1.3 75.2 - - - +
251A PHE* 1.3 63.6 + - - +
253A ASN 3.2 4.2 + - - -
254A PHE* 3.2 19.8 + - - +
257A LEU* 3.8 6.4 - - + +
269A ALA* 3.7 43.1 - - + +
270A ALA* 4.1 8.3 - - - -
271A GLN* 4.1 23.8 - - + +
296A GLU* 4.4 5.4 - - + +
298A GLU* 3.6 34.5 - - + -
300A PHE* 4.0 12.9 - - + -
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Residues in contact with PHE 251 (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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247A ALA* 3.0 24.6 + - + -
248A GLN* 3.2 16.6 + - - +
250A ILE* 1.3 76.5 - - + +
252A LEU* 1.3 63.4 + - - +
254A PHE* 3.0 20.3 + - - +
298A GLU* 3.2 32.1 - - + -
300A PHE* 4.1 21.1 - + - -
413A TYR* 3.6 30.7 - + - -
414A ASP* 3.6 37.0 - - + -
415A LEU* 3.9 19.1 - - + +
418A HIS* 4.2 14.1 - - + -
426A LEU* 4.1 7.6 - - - +
522A GLU* 3.5 11.9 - - - -
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Residues in contact with LEU 252 (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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130A THR* 6.1 0.2 - - + -
134A VAL* 3.9 34.3 - - + -
248A GLN 2.8 22.7 + - - +
249A GLY* 3.8 9.9 - - - +
251A PHE* 1.3 75.4 - - - +
253A ASN* 1.3 62.6 + - - +
254A PHE 3.4 0.9 + - - -
255A LYS* 5.1 2.1 + - - +
256A ARG* 4.6 7.8 + - - +
418A HIS* 4.0 33.9 - - + +
422A THR* 6.0 4.9 - - + -
426A LEU* 5.4 7.9 - - + +
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Residues in contact with ASN 253 (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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124A ILE* 3.6 8.2 - - + +
126A CYS* 3.2 24.7 - - - -
249A GLY* 2.6 24.9 + - - +
250A ILE 3.2 6.3 + - - +
251A PHE 3.1 0.8 - - - -
252A LEU* 1.3 80.5 - - - +
254A PHE* 1.3 62.7 + - - +
255A LYS 3.3 2.7 - - - -
256A ARG* 2.7 47.6 + - + +
257A LEU* 3.0 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