Contacts of the helix formed by residues 247 - 258 (chain A) in PDB entry 3KCZ
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A LYS 3.3 13.5 + - - +
244A LEU* 3.5 18.3 - - + +
245A ILE 3.3 3.1 - - - +
246A CYS* 1.3 72.5 - - - +
248A VAL* 1.3 61.5 + - - +
249A GLN* 3.1 16.3 + - - +
250A ALA* 3.0 31.2 + - + +
251A MET* 3.3 23.0 + - - +
254A MET* 5.3 0.2 - - - +
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Residues in contact with VAL 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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246A CYS 3.1 12.5 + - - +
247A ASN* 1.3 70.0 + - - +
249A GLN* 1.3 65.6 + - - +
250A ALA 3.1 1.8 - - - -
251A MET* 3.0 19.4 + - + +
252A GLU* 3.0 22.6 + - + +
267A LEU* 5.3 6.3 - - + -
343A ALA* 5.7 1.1 - - + +
344A ILE* 4.5 26.5 - - + -
347A VAL* 4.3 22.2 - - + -
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Residues in contact with GLN 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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247A ASN* 3.1 10.1 + - - +
248A VAL* 1.3 79.8 - - - +
250A ALA* 1.3 56.8 + - - +
252A GLU* 3.3 16.6 - - - +
253A GLU* 2.8 57.9 + - - +
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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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244A LEU* 5.4 2.7 - - + +
247A ASN* 3.0 31.2 + - + +
248A VAL 3.1 0.4 - - - -
249A GLN* 1.3 74.9 - - - +
251A MET* 1.3 60.4 + - - +
253A GLU* 3.4 12.3 + - - +
254A MET* 2.9 46.6 + - + +
480A LYS* 6.0 4.3 - - + +
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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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245A ILE 3.4 25.4 - - - +
246A CYS* 4.7 5.4 - - - -
247A ASN 3.6 12.6 - - - +
248A VAL* 3.0 23.6 + - + +
250A ALA* 1.3 77.7 - - - +
252A GLU* 1.3 57.6 + - - +
254A MET* 3.3 10.0 + - + +
255A MET* 2.9 35.0 + - - +
267A LEU* 4.1 7.0 - - + -
340A ILE* 3.8 35.7 - - + +
343A ALA* 3.5 31.2 - - + -
344A ILE* 5.2 0.9 - - - -
433A SER* 3.8 27.1 - - - +
436A VAL* 4.8 1.8 - - + -
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Residues in contact with GLU 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 VAL* 3.0 13.6 + - + +
249A GLN* 3.3 25.8 - - - +
251A MET* 1.3 73.4 - - - +
253A GLU* 1.3 66.0 + - + +
255A MET* 3.3 2.6 + - - +
256A MET* 3.0 39.7 + - - +
262A THR* 3.1 34.9 + - - +
263A LYS* 4.4 11.4 + - - +
266A PRO* 5.8 0.5 - - - +
267A LEU* 3.8 22.1 + - + +
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Residues in contact with GLU 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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249A GLN* 2.8 47.1 + - - +
250A ALA* 3.8 9.8 - - - +
251A MET 3.4 0.2 - - - -
252A GLU* 1.3 81.2 - - + +
254A MET* 1.3 62.5 + - + +
256A MET* 3.4 12.5 + - - +
257A GLU* 3.0 26.9 + - + +
480A LYS* 3.7 26.2 + - + +
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Residues in contact with MET 254 (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 ASN 5.3 0.4 - - - +
250A ALA* 2.9 46.1 + - + +
251A MET* 3.6 14.6 - - + +
253A GLU* 1.3 77.7 - - + +
255A MET* 1.3 72.8 + - + +
257A GLU* 3.3 10.8 - - - +
258A MET* 3.2 26.1 + - + +
431A ARG* 4.9 6.3 - - - +
432A MET* 3.7 24.7 - - + +
433A SER* 3.4 38.4 - - - +
480A LYS* 6.2 4.5 - - + -
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Residues in contact with MET 255 (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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251A MET 2.9 13.1 + - - +
252A GLU 3.9 3.1 - - - +
254A MET* 1.3 86.7 - - + +
256A MET* 1.3 66.8 + - - +
258A MET* 3.0 37.0 + - - +
260A TYR* 3.1 31.6 + - + +
262A THR* 4.1 11.4 - - + -
267A LEU* 4.1 12.1 - - + -
333A LEU* 4.0 15.3 - - - -
336A ALA* 3.8 18.2 - - + -
337A LEU* 4.0 15.7 - - + -
340A ILE* 3.3 33.0 - - + -
431A ARG* 5.4 0.9 - - - -
433A SER* 4.3 4.9 - - - +
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Residues in contact with MET 256 (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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252A GLU* 3.0 30.5 + - - +
253A GLU* 3.7 10.3 - - - +
255A MET* 1.3 74.7 - - - +
257A GLU* 1.3 57.1 + - - +
259A LYS* 2.8 26.3 + - - +
260A TYR 3.8 9.6 - - - +
262A THR* 3.2 27.8 - - + +
263A LYS* 3.8 22.4 - - - +
312A ASP* 6.0 2.0 - - - +
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Residues in contact with GLU 257 (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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253A GLU* 3.0 18.0 + - + +
254A MET* 3.3 13.9 - - - +
255A MET 3.2 0.2 - - - -
256A MET* 1.3 77.0 - - - +
258A MET* 1.3 59.1 + - + +
259A LYS* 3.2 17.3 + - - +
479A LEU* 5.8 4.7 - - - +
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Residues in contact with MET 258 (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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254A MET* 3.2 12.1 + - - +
255A MET* 3.0 37.0 + - - +
257A GLU* 1.3 76.1 - - + +
259A LYS* 1.3 69.5 + - - +
260A TYR 3.3 3.6 + - - -
329A GLU 4.6 5.2 - - - +
330A LYS* 4.4 7.3 + - - -
332A GLN* 4.1 3.6 - - + -
333A LEU* 3.7 52.5 - - + +
336A ALA* 4.6 1.3 - - - -
431A ARG* 3.5 50.9 - - - +
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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