Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 5AJQ
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PHE* 5.8 0.9 - - - -
239A GLU 4.1 0.6 - - - -
240A LEU* 1.3 77.9 - - - +
242A PRO* 1.3 70.3 - - + +
243A MET* 3.2 12.0 + - - +
244A ARG* 2.9 31.2 + - - +
245A VAL* 2.9 26.2 + - - +
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Residues in contact with PRO 242 (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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192A PHE* 3.6 30.1 - - + +
195A THR* 3.0 37.2 - - + +
196A PRO* 5.3 2.8 - - + +
197A TYR* 5.9 0.2 - - - +
240A LEU 3.9 0.9 - - - +
241A ASN* 1.3 90.4 - - + +
243A MET* 1.3 62.7 + - + +
245A VAL* 3.4 10.0 + - - +
246A LEU* 3.5 20.8 + - - +
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Residues in contact with MET 243 (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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205A MET* 5.8 3.1 - - - -
241A ASN* 3.2 7.9 + - - +
242A PRO* 1.3 78.7 - - + +
244A ARG* 1.3 66.3 + - - +
246A LEU* 3.3 35.3 + - + +
247A LEU* 3.5 26.3 + - + +
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Residues in contact with ARG 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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240A LEU* 4.0 29.6 - - + -
241A ASN* 2.9 30.4 + - - +
243A MET* 1.3 77.5 - - - +
245A VAL* 1.3 57.9 + - - +
247A LEU* 3.4 31.1 + - - +
248A LYS* 2.9 27.5 + - - +
1313A CL 3.1 29.1 - - - +
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Residues in contact with VAL 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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195A THR* 3.8 11.2 - - + -
196A PRO 4.4 2.5 - - - +
197A TYR* 3.5 43.3 - - + -
237A HIS* 3.6 20.4 - - + +
240A LEU* 3.6 12.1 - - + +
241A ASN 2.9 18.3 + - - +
242A PRO 3.6 9.0 - - - +
243A MET 3.2 0.4 - - - -
244A ARG* 1.3 73.3 - - - +
246A LEU* 1.3 66.5 + - + +
248A LYS* 3.2 6.7 + - - +
249A ILE* 2.9 49.0 + - + +
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Residues in contact with LEU 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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196A PRO* 3.6 32.3 - - + +
199A MET* 3.8 0.4 - - + -
204A VAL* 3.5 45.5 - - + +
205A MET* 4.0 25.1 - - + -
242A PRO 3.5 14.1 - - - +
243A MET* 3.3 29.6 + - + +
245A VAL* 1.3 78.2 - - + +
247A LEU* 1.3 57.0 + - - +
249A ILE* 3.3 1.0 + - - +
250A ALA* 3.1 23.7 + - - +
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Residues in contact with LEU 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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205A MET* 3.8 22.7 - - + -
243A MET* 3.5 27.6 + - + +
244A ARG* 3.8 31.4 - - - +
245A VAL 3.2 0.4 - - - -
246A LEU* 1.3 77.5 - - - +
248A LYS* 1.3 66.9 + - - +
250A ALA* 3.4 3.9 + - - +
251A LYS* 3.0 27.5 + - - +
1313A CL 4.0 11.2 - - + -
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Residues in contact with LYS 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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237A HIS* 3.4 38.8 + - + +
240A LEU* 4.0 16.1 - - + +
244A ARG* 2.9 19.8 + - - +
245A VAL* 3.2 8.7 + - - +
247A LEU* 1.3 78.4 - - - +
249A ILE* 1.3 56.8 + - - +
251A LYS* 5.0 0.4 - - - +
252A SER* 2.5 51.7 + - - +
1313A CL 3.6 18.4 - - + +
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Residues in contact with ILE 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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196A PRO 3.4 25.4 - - - +
197A TYR* 3.9 13.7 - - - +
199A MET 3.5 21.3 - - - +
201A PRO* 3.8 28.2 - - + +
204A VAL* 4.0 14.6 - - + -
221A TRP* 4.9 10.8 - - + +
237A HIS* 4.1 19.5 - - + -
245A VAL* 2.9 32.0 + - + +
246A LEU* 3.7 4.0 - - + +
248A LYS* 1.3 74.9 - - - +
250A ALA* 1.3 66.3 + - - +
251A LYS 3.3 0.3 + - - -
252A SER* 3.8 7.1 + - - +
277A LYS* 3.9 5.4 + - - -
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Residues in contact with ALA 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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201A PRO* 4.4 12.9 - - - +
204A VAL* 4.0 14.1 - - + +
205A MET* 4.4 8.3 - - + -
246A LEU 3.1 16.8 + - - +
247A LEU* 3.6 8.5 - - - +
249A ILE* 1.3 77.0 - - - +
251A LYS* 1.3 55.2 + - + +
277A LYS* 2.7 25.1 + - - -
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Residues in contact with LYS 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 LEU* 3.0 16.2 + - + +
248A LYS* 4.4 0.9 - - - +
250A ALA* 1.3 78.4 - - + +
252A SER* 1.3 69.1 + - - +
253A ASP* 3.8 1.0 + - - +
277A LYS* 3.6 3.8 + - - -
1313A CL 3.8 23.1 - - + -
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Residues in contact with SER 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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237A HIS* 4.6 10.3 - - - -
248A LYS* 2.5 49.9 + - - +
249A ILE* 3.8 4.5 + - - +
250A ALA 3.7 0.4 - - - -
251A LYS* 1.3 81.2 - - - +
253A ASP* 1.3 72.8 + - - +
254A PRO* 4.7 0.2 - - - +
277A LYS* 2.8 25.3 + - - +
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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