Contacts of the helix formed by residues 243 - 252 (chain A) in PDB entry 3CQ6
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 ASN 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ASN* 4.3 0.9 - - - -
213A LEU* 4.7 6.3 - - + +
217A PRO* 3.5 35.8 - - + +
220A LEU 4.8 0.4 + - - -
242A ALA* 1.3 76.7 - - - +
244A PRO* 1.3 71.9 - - - +
245A ALA* 3.1 15.1 + - - +
246A PHE* 2.8 31.7 + - + +
247A ILE* 4.0 1.4 + - - +
4C ILE* 3.4 40.4 + - - +
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Residues in contact with PRO 244 (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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90A ASP* 3.1 42.0 - - + +
91A ASN* 3.5 16.2 - - - +
242A ALA 3.7 0.2 - - - -
243A ASN* 1.3 95.5 - - - +
245A ALA* 1.3 59.9 + - - +
246A PHE 3.1 0.4 - - - -
247A ILE* 3.0 16.1 + - + +
248A ASP* 3.3 16.1 + - - +
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Residues in contact with ALA 245 (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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243A ASN* 2.8 19.8 + - + +
244A PRO* 1.3 73.9 - - - +
246A PHE* 1.3 57.8 + - - +
248A ASP* 3.3 12.9 + - - +
249A ALA 3.0 21.7 + - - -
4C ILE* 4.1 4.9 - - + +
5C THR* 3.8 29.6 - - - -
6C LEU* 3.6 10.2 - - - +
9C LEU* 3.5 21.8 - - + -
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Residues in contact with PHE 246 (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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105A LEU* 4.7 2.5 - - + -
109A PHE* 3.6 35.2 - + - -
193A ILE* 4.0 16.4 - - + -
217A PRO 3.3 24.9 - - - -
218A THR 3.9 12.8 - - - -
219A LYS 4.3 3.6 - - - -
220A LEU 3.9 10.5 - - - -
221A VAL* 3.5 25.6 - - + -
240A PHE* 4.0 10.3 - - + -
242A ALA* 3.7 20.6 - - + -
243A ASN* 2.8 20.7 + - + +
245A ALA* 1.3 78.4 - - - +
247A ILE* 1.3 57.4 + - - +
249A ALA* 3.2 4.7 + - - +
250A VAL* 3.0 32.1 + - - +
9C LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 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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72A ARG* 3.9 17.9 - - - +
90A ASP* 3.5 23.8 - - - +
91A ASN 3.7 14.8 - - - +
92A LEU 3.6 18.2 - - - +
93A TRP* 4.1 15.9 - - + -
240A PHE* 3.6 24.0 - - + -
242A ALA 4.8 0.2 - - - +
243A ASN 4.1 10.1 - - - +
244A PRO 3.0 8.5 + - - +
246A PHE* 1.3 74.3 - - - +
248A ASP* 1.3 69.9 + - - +
250A VAL* 3.5 6.8 + - - +
251A MET* 3.2 40.6 + - - +
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Residues in contact with ASP 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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244A PRO* 3.3 13.1 + - - +
245A ALA* 3.3 15.0 + - - +
247A ILE* 1.3 82.0 - - - +
249A ALA* 1.3 61.8 + - - +
251A MET* 3.4 18.8 + - - +
252A LEU* 3.7 13.9 + - - +
6C LEU* 4.2 23.7 + - + +
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Residues in contact with ALA 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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108A ALA* 4.3 9.3 - - - +
109A PHE* 3.6 33.9 - - + -
245A ALA 3.0 8.1 + - - +
246A PHE 3.3 9.9 - - - +
247A ILE 3.2 0.2 - - - -
248A ASP* 1.3 75.8 - - - +
250A VAL* 1.3 63.0 + - - +
252A LEU* 3.2 21.3 + - - +
253A VAL* 4.0 2.3 + - - +
6C LEU* 3.7 22.6 - - + +
11C LEU* 4.1 10.4 - - + +
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Residues in contact with VAL 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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93A TRP* 3.6 40.6 - - + +
104A GLN* 4.3 21.1 - - + +
105A LEU* 3.8 28.7 - - + -
108A ALA* 4.8 3.1 - - + -
240A PHE* 4.0 7.9 - - + -
246A PHE 3.0 19.2 + - - +
247A ILE* 3.6 9.2 - - - +
249A ALA* 1.3 75.8 - - + +
251A MET* 1.3 62.0 + - - +
252A LEU 3.2 0.2 - - - -
253A VAL* 3.1 12.0 + - + +
254A ARG* 2.9 31.9 + - - +
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Residues in contact with MET 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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67A ASP* 4.2 22.9 - - - +
72A ARG* 5.9 2.5 - - - -
93A TRP* 4.0 26.2 - - + -
247A ILE* 3.2 34.2 + - - +
248A ASP* 3.6 12.1 - - - +
249A ALA 3.2 0.4 - - - -
250A VAL* 1.3 77.4 - - - +
252A LEU* 1.3 59.2 + - + +
253A VAL 3.3 0.6 + - - -
254A ARG* 3.6 30.6 + - - +
20C ALA* 3.3 35.4 - - + +
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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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248A ASP 3.7 11.7 - - - +
249A ALA 3.2 10.1 + - - +
250A VAL 3.2 0.6 - - - -
251A MET* 1.3 78.1 - - - +
253A VAL* 1.3 59.3 - - + +
254A ARG 5.1 0.8 - - - +
6C LEU* 4.3 14.1 - - + -
11C LEU* 4.0 19.1 - - + -
15C LEU* 3.5 45.3 - - + +
18C GLU* 3.5 23.3 - - + +
19C HIS 3.8 2.7 - - - -
20C ALA* 3.5 31.5 - - + +
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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