Contacts of the helix formed by residues 344 - 353 (chain B) in PDB entry 3CM7
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 LEU 344 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B ASN* 2.7 24.8 + - + +
341B ASN* 4.5 7.9 - - - +
342B ILE 3.4 0.4 - - - -
343B HIS* 1.3 80.0 - - + +
345B THR* 1.3 58.2 + - - +
347B SER* 3.6 9.3 - - - +
348B LEU* 3.3 21.0 + - - +
341D ASN* 3.9 24.5 - - - +
344D LEU* 4.7 17.5 - - + +
345D THR* 4.6 21.8 - - + +
348D LEU* 3.8 30.3 - - + +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN 3.1 23.1 - - - +
342B ILE* 3.1 19.3 - - - +
344B LEU* 1.3 77.4 - - - +
346B HIS* 1.3 62.0 + - - +
347B SER 3.2 0.9 - - - -
348B LEU* 3.4 8.5 - - - +
349B GLU* 2.8 34.2 + - - +
600C X22 4.2 40.8 + - + +
344D LEU* 4.0 17.6 - - - +
700D X22 4.2 9.8 - - + +
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Residues in contact with HIS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 3.8 15.7 + - - -
322B LYS* 3.1 41.3 - - + +
342B ILE* 2.8 36.1 + - + +
343B HIS* 4.8 8.1 - - + +
345B THR* 1.3 79.5 - - + +
347B SER* 1.3 61.6 + - - +
349B GLU* 3.5 16.5 + - - +
350B GLU* 3.2 33.8 + - - +
600C X22 4.3 16.5 - + - -
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B HIS 2.6 24.8 + - - -
344B LEU* 3.6 13.7 - - - +
345B THR 3.7 0.4 - - - +
346B HIS* 1.3 79.9 - - - +
348B LEU* 1.3 62.5 + - - +
350B GLU* 3.5 13.2 + - - +
351B CYS* 3.4 18.7 + - - +
354B ARG* 4.7 1.0 + - - -
348D LEU* 4.2 18.4 - - - +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B LEU 3.3 10.5 + - - +
345B THR* 3.2 11.6 + - - +
346B HIS 3.2 0.2 - - - -
347B SER* 1.3 77.0 - - - +
349B GLU* 1.3 67.1 + - - +
351B CYS* 3.0 6.5 + - - +
352B LEU* 2.8 58.1 + - + +
323C TRP* 4.2 18.8 - - + -
600C X22 4.3 6.3 - - + -
344D LEU* 4.0 24.9 - - + +
347D SER* 3.8 30.3 - - - +
348D LEU* 4.3 22.4 - - + +
351D CYS* 5.7 1.8 - - + -
700D X22 5.2 0.2 - - + -
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Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR 2.8 19.0 + - - +
346B HIS* 3.5 18.9 - - + +
348B LEU* 1.3 73.3 - - - +
350B GLU* 1.3 60.7 + - + +
352B LEU* 3.3 5.9 + - - +
353B VAL* 3.1 38.3 + - - +
308C THR* 6.4 0.7 - - - -
309C ASP* 3.9 13.1 - - - +
600C X22 3.6 48.3 + - + +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B HIS* 3.2 22.3 + - - +
347B SER* 3.7 10.6 - - - +
348B LEU 3.2 0.2 - - - -
349B GLU* 1.3 77.8 - - + +
351B CYS* 1.3 62.3 + - - +
353B VAL* 3.2 6.9 + - - +
354B ARG* 3.1 42.2 + - - +
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Residues in contact with CYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B SER 3.4 9.0 + - - +
348B LEU* 3.0 10.4 + - - +
350B GLU* 1.3 78.8 - - - +
352B LEU* 1.3 59.9 + - - +
353B VAL 3.3 0.9 + - - -
354B ARG* 3.1 30.0 + - - +
355B THR* 3.5 14.5 - - - +
348D LEU* 4.8 0.9 - - + -
351D CYS* 2.1 57.4 - - + -
352D LEU* 3.3 29.4 - - + -
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU* 2.8 41.7 + - + +
349B GLU* 3.7 6.7 - - - +
350B GLU 3.2 0.2 - - - -
351B CYS* 1.3 77.7 - - - +
353B VAL* 1.3 63.5 + - + +
354B ARG 3.6 0.2 - - - -
355B THR* 3.6 21.7 + - + +
322C LYS* 5.7 2.7 - - - +
323C TRP* 3.9 21.1 - - + -
350C GLU* 5.9 2.2 - - - +
600C X22 3.9 16.8 - - + +
351D CYS* 3.7 22.4 - - + -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLU* 3.1 32.2 + - - +
350B GLU* 3.2 6.5 + - - +
351B CYS 3.2 0.2 - - - -
352B LEU* 1.3 84.2 - - + +
354B ARG* 1.3 61.1 + - - +
355B THR* 4.6 1.3 - - - +
309C ASP* 6.4 2.0 - - + -
311C LYS* 4.9 18.6 - - - +
600C X22 5.0 7.4 - - - +
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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