Contacts of the helix formed by residues 407 - 415 (chain A) in PDB entry 3KMR
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 PRO 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A TRP* 4.6 5.2 - - + +
229A SER* 4.1 22.0 - - - +
230A GLU* 6.1 0.2 - - - -
233A THR* 3.9 19.7 - - + +
405A SER 3.7 3.8 - - - +
406A MET* 1.3 89.6 - - + +
408A PRO* 1.4 75.3 - - + +
409A LEU 3.3 1.8 - - - +
410A ILE* 3.1 28.6 + - + +
411A GLN* 3.0 19.1 + - - +
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A MET 3.6 2.9 - - - +
407A PRO* 1.4 85.1 - - + -
409A LEU* 1.3 56.8 + - - +
411A GLN* 3.2 14.9 + - + +
412A GLU* 3.0 29.9 + - + +
631C ILE* 3.7 21.1 - - + -
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Residues in contact with LEU 409 (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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233A THR* 3.9 25.3 - - + +
236A ILE* 3.7 27.1 - - + -
237A ILE* 3.7 28.7 - - + -
407A PRO* 3.3 1.4 - - - +
408A PRO* 1.3 79.2 - - - +
410A ILE* 1.3 62.9 + - - +
412A GLU* 3.1 8.6 + - + +
413A MET* 3.0 44.4 + - - +
631C ILE* 3.9 32.2 - - + +
632C LEU* 4.6 6.1 - - + +
635C LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 410 (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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1A EQN 4.5 11.7 - - + -
229A SER* 3.7 29.2 - - - +
232A SER* 4.1 12.6 - - - -
233A THR* 3.8 11.7 - - - +
236A ILE* 3.9 24.2 - - + -
395A VAL* 6.1 0.7 - - + -
406A MET* 3.9 26.2 - - + -
407A PRO* 3.1 26.3 + - + +
409A LEU* 1.3 74.8 - - - +
411A GLN* 1.3 57.5 + - - +
413A MET* 3.2 1.5 + - - -
414A LEU* 2.8 53.2 + - + +
415A GLU* 4.7 0.8 - - + +
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Residues in contact with GLN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 3.9 18.8 + - - -
406A MET* 3.0 38.5 + - + +
407A PRO 3.0 7.1 + - - +
408A PRO* 3.2 13.8 + - + +
410A ILE* 1.3 77.1 - - - +
412A GLU* 1.3 58.5 + - + +
415A GLU* 2.9 57.3 + - + +
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Residues in contact with GLU 412 (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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262A LYS* 3.1 28.2 + - - +
408A PRO* 3.0 17.7 + - + +
409A LEU* 3.1 12.7 + - + +
411A GLN* 1.3 75.8 - - + +
413A MET* 1.3 60.4 + - - +
415A GLU 4.2 0.7 - - - +
629C HIS* 3.2 26.7 - - + -
630C LYS* 3.4 16.1 + - - +
631C ILE* 2.8 40.2 + - - +
632C LEU* 2.9 28.9 + - + +
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Residues in contact with MET 413 (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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236A ILE* 3.7 34.3 - - + -
240A VAL* 5.5 1.1 - - + -
261A LEU* 3.5 46.0 - - + +
262A LYS* 3.1 35.8 + - + +
265A CYS* 3.9 20.4 - - + -
409A LEU* 3.0 25.3 + - + +
410A ILE 3.8 3.1 - - - +
412A GLU* 1.3 78.4 - - - +
414A LEU* 1.3 64.8 + - + +
632C LEU* 3.8 31.2 - - + -
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Residues in contact with LEU 414 (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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1A EQN 3.7 29.8 - - + -
236A ILE* 5.9 0.4 - - + -
262A LYS* 4.6 4.7 - - - +
265A CYS* 4.0 25.6 - - + -
266A LEU* 4.0 21.5 - - + +
395A VAL* 3.9 35.7 - - + +
410A ILE* 2.8 31.5 + - + +
413A MET* 1.3 83.6 - - + +
415A GLU* 1.3 69.5 + - + +
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Residues in contact with GLU 415 (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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262A LYS* 2.9 26.0 + - - -
395A VAL* 3.6 14.2 - - - +
399A LYS* 3.1 41.4 - - - +
406A MET* 5.3 4.3 - - + +
410A ILE* 4.7 0.7 - - + +
411A GLN* 2.9 48.4 + - + +
412A GLU 4.2 0.9 - - - +
414A LEU* 1.3 81.5 - - + +
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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