Contacts of the helix formed by residues 295 - 302 (chain A) in PDB entry 3IKM
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 MET 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ASN* 4.4 5.4 - - + -
271A VAL* 3.0 49.8 - - + +
293A ASP* 3.9 8.1 - - - +
294A THR* 1.3 82.0 + - - +
296A SER* 1.3 66.3 + - - +
298A HIS* 3.2 9.3 + - - +
299A MET* 3.0 26.2 + - + +
353A VAL* 3.0 36.3 - - + -
354A ASN* 3.5 15.9 - - - +
358A LEU* 4.5 10.5 - - + -
845A VAL* 4.3 18.8 - - + -
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Residues in contact with SER 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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292A LEU* 5.4 0.2 - - - +
293A ASP* 2.6 32.8 + - - +
295A MET* 1.3 79.0 - - - +
297A MET* 1.3 66.0 + - - +
299A MET* 2.7 26.9 + - - +
300A ALA 2.8 9.5 + - - -
427A MET* 4.9 3.3 - - - +
845A VAL* 4.4 0.4 - - - -
846A THR* 2.4 45.3 + - - -
847A ALA* 3.2 13.8 - - - +
848A GLY 3.8 4.9 - - - +
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Residues in contact with MET 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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292A LEU* 5.7 3.6 - - + +
293A ASP 3.1 15.5 - - - +
294A THR* 3.0 19.5 - - - +
296A SER* 1.3 80.9 + - - +
298A HIS* 1.3 61.7 + - - +
300A ALA* 2.8 13.6 - - - +
301A ILE* 2.5 37.4 + - - +
362A HIS* 6.3 0.2 - - - -
407A PHE* 5.1 0.4 - - - -
411A LEU* 2.8 67.8 - - + -
415A LEU* 3.2 29.7 - - + +
427A MET* 5.6 5.6 - - + +
847A ALA* 4.7 0.9 - - - -
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Residues in contact with HIS 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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294A THR 3.6 12.8 - - - +
295A MET* 3.2 13.1 + - - +
297A MET* 1.3 79.8 - - - +
299A MET* 1.3 111.2 + - - +
301A ILE* 2.9 5.3 + - - +
302A SER* 2.6 55.2 + - - +
303A GLY* 4.0 2.2 - - - -
309A ARG* 4.1 0.7 - - - -
351A SER* 2.5 38.6 + - - -
353A VAL* 3.5 10.0 - - - -
358A LEU* 3.0 37.9 - - + +
362A HIS* 5.4 6.7 - - + +
407A PHE* 5.6 0.2 - - + -
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Residues in contact with MET 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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295A MET* 3.1 17.9 - - + +
296A SER 2.7 13.2 + - - +
298A HIS* 1.3 105.2 + - - +
300A ALA* 1.3 61.7 + - - +
303A GLY* 3.2 18.5 + - - -
309A ARG* 4.2 12.8 - - - +
353A VAL* 3.1 40.2 - - + -
848A GLY* 3.6 20.0 - - - +
849A THR 3.3 34.1 - - - +
850A ILE* 4.9 8.9 - - - +
1024A ASP* 5.5 0.3 - - - +
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Residues in contact with ALA 300 (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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296A SER 2.8 6.8 + - - +
297A MET* 2.8 24.7 + - - +
299A MET* 1.3 78.6 - - - +
301A ILE* 1.3 57.1 + - + +
415A LEU* 5.1 5.2 - - + -
427A MET* 6.2 1.8 - - + -
847A ALA* 4.4 9.4 - - + +
849A THR 4.9 0.2 + - - -
850A ILE 5.4 3.0 - - - +
852A ARG* 4.7 24.3 + - - +
1022A LEU 4.2 13.9 - - - +
1023A GLN* 5.5 1.2 - - - -
1024A ASP* 4.8 4.0 - - - +
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Residues in contact with ILE 301 (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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297A MET 2.5 19.2 + - - +
298A HIS* 2.9 5.3 + - - +
300A ALA* 1.3 73.2 - - - +
302A SER* 1.3 74.4 + - - +
303A GLY 3.5 0.7 - - - -
362A HIS* 4.9 12.8 - - + +
411A LEU* 6.2 0.4 - - - -
414A PHE* 2.8 64.4 - - + +
415A LEU* 3.4 16.2 - - + +
417A ARG* 4.9 0.7 - - + -
418A CYS* 4.6 13.5 - - - -
1022A LEU 5.6 1.1 - - - -
1024A ASP* 2.3 40.0 - - + +
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Residues in contact with SER 302 (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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298A HIS* 2.6 40.5 + - - +
301A ILE* 1.3 88.9 - - - +
303A GLY* 1.3 56.4 + - - +
349A ASP* 4.9 7.0 - - - -
351A SER* 2.9 30.8 - - - -
361A VAL* 5.0 8.9 - - - +
362A HIS* 4.3 10.4 + - - -
1024A ASP* 3.7 4.3 - - - -
1025A LEU* 5.4 0.2 - - - -
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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