Contacts of the helix formed by residues 398 - 412 (chain B) in PDB entry 5MKE
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 THR 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B SER* 2.9 38.3 + - - +
397B ARG* 1.3 77.2 - - - +
399B ARG* 1.3 59.8 + - - +
400B GLU* 2.2 35.9 + - - +
401B GLU* 4.0 19.7 - - + +
402B THR* 3.1 7.3 - - - +
543B ASN* 5.8 1.0 - - - +
1001B NAG 3.8 27.3 + - - -
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Residues in contact with ARG 399 (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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288B LEU* 3.5 37.4 + - + +
289B ASP* 4.5 2.5 - - - +
291B LEU* 2.7 33.5 + - - +
292B TYR* 4.3 4.9 + - - +
293B TRP* 3.2 61.5 - - + +
315B LEU* 5.7 5.1 - - - +
395B LEU* 5.1 6.7 - - - +
396B SER 4.1 6.2 + - - -
397B ARG* 3.3 21.9 + - - +
398B THR* 1.3 71.0 - - - +
400B GLU* 1.3 73.6 + - - +
402B THR* 3.2 26.2 + - - +
403B ALA* 4.1 5.9 + - - +
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B THR* 2.2 33.1 + - - +
399B ARG* 1.3 82.2 + - - +
401B GLU* 1.3 70.6 + - + +
403B ALA* 3.4 10.7 + - - +
404B ALA* 3.5 7.2 + - - +
1001B NAG 4.7 4.6 + - - -
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Residues in contact with GLU 401 (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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396B SER* 5.0 0.9 - - - +
398B THR* 4.0 14.4 - - + +
400B GLU* 1.3 82.5 - - + +
402B THR* 1.3 58.0 + - - +
403B ALA 3.0 2.2 - - - -
404B ALA* 2.6 20.4 + - + -
405B GLN* 2.3 47.7 + - + +
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Residues in contact with THR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 3.3 30.1 - - + +
395B LEU* 3.1 25.2 - - - +
396B SER* 3.1 27.1 + - - -
398B THR 3.1 15.0 - - - +
399B ARG* 3.2 27.1 + - - +
401B GLU* 1.3 76.2 - - - +
403B ALA* 1.3 61.4 + - - +
405B GLN* 3.5 16.4 - - - +
406B VAL* 3.7 17.7 - - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B GLU* 6.5 0.4 - - + -
288B LEU* 4.3 18.8 - - + -
399B ARG 4.4 5.2 - - - +
400B GLU 3.4 9.1 + - - +
401B GLU 3.0 0.6 - - - -
402B THR* 1.3 83.3 - - - +
404B ALA* 1.3 52.0 + - - +
405B GLN 3.2 0.4 - - - -
406B VAL* 3.1 11.2 + - - +
407B ALA* 2.6 32.8 + - - +
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Residues in contact with ALA 404 (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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400B GLU 3.5 3.9 + - - +
401B GLU* 2.6 35.7 + - + +
403B ALA* 1.3 71.1 - - - +
405B GLN* 1.3 53.0 + - - +
407B ALA* 3.1 12.9 - - + +
408B SER* 2.2 39.0 + - - -
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Residues in contact with GLN 405 (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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321B ILE* 5.4 0.5 - - - +
393B LEU* 3.9 24.0 - - + +
394B ASP 3.9 18.8 + - - -
395B LEU* 3.2 28.2 - - - +
396B SER* 4.2 15.9 - - - -
401B GLU* 2.3 33.9 + - + +
402B THR* 3.5 15.5 - - - +
404B ALA* 1.3 66.5 - - - +
406B VAL* 1.3 50.6 - - + +
408B SER* 2.8 9.9 + - - -
409B LEU* 2.2 45.5 + - + +
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Residues in contact with VAL 406 (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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280B TRP* 4.4 0.7 - - + -
283B THR* 4.3 28.9 - - + +
284B GLU* 5.6 4.0 - - + +
288B LEU* 5.9 3.6 - - + -
402B THR 3.7 13.7 - - - +
403B ALA* 3.1 13.5 + - - +
405B GLN* 1.3 75.6 - - + +
407B ALA* 1.3 51.4 + - - +
409B LEU* 3.0 21.1 + - + +
410B LYS 2.5 29.6 + - - -
414B TRP* 3.2 29.2 - - + +
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Residues in contact with ALA 407 (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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403B ALA 2.6 12.4 + - - +
404B ALA* 3.0 21.1 + - + +
406B VAL* 1.3 71.0 - - - +
408B SER* 1.3 58.9 + - - +
409B LEU 3.1 0.2 - - - -
410B LYS* 3.0 11.7 + - - +
411B LYS* 2.8 23.6 + - - +
414B TRP* 5.3 0.2 - - - -
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Residues in contact with SER 408 (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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362B ASN* 4.0 7.4 + - - -
404B ALA 2.2 30.4 + - - -
405B GLN* 3.3 10.1 - - - -
407B ALA* 1.3 68.0 - - - +
409B LEU* 1.3 50.7 + - - +
410B LYS 3.3 0.2 - - - -
411B LYS* 3.1 12.6 - - - +
412B ASN* 2.7 37.8 + - - -
1002B NAG 3.5 32.1 + - - -
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Residues in contact with LEU 409 (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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321B ILE* 5.9 5.8 - - + -
365B ALA* 6.0 2.5 - - + -
393B LEU* 5.8 8.3 - - + -
405B GLN* 2.2 32.1 + - + +
406B VAL* 3.1 29.6 - - + +
408B SER* 1.3 68.7 - - - +
410B LYS* 1.3 53.1 + - - +
412B ASN* 3.4 13.9 - - + +
413B VAL 2.5 10.0 + - - -
414B TRP* 2.2 78.5 + - + +
415B LEU* 4.4 21.3 - - + -
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Residues in contact with LYS 410 (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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406B VAL 2.5 13.2 + - - +
407B ALA* 3.1 13.2 - - - +
409B LEU* 1.3 69.8 - - - +
411B LYS* 1.3 59.8 + - - +
412B ASN 3.0 1.6 - - - -
413B VAL* 2.6 34.5 + - + +
414B TRP* 3.4 33.4 - - + -
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Residues in contact with LYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 4.0 12.4 - - - +
407B ALA 2.8 11.7 + - - +
408B SER* 3.1 22.7 - - - +
410B LYS* 1.3 73.2 - - - +
412B ASN* 1.3 62.0 + - - +
413B VAL* 4.8 2.6 - - - +
1002B NAG 2.9 58.5 + - - +
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Residues in contact with ASN 412 (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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360B PRO* 3.4 36.9 + - + +
362B ASN* 5.0 4.8 - - - +
365B ALA* 3.8 24.7 - - + +
366B TRP* 4.8 5.8 - - + -
408B SER* 2.7 27.0 + - - +
409B LEU* 3.3 17.9 + - + +
410B LYS 3.0 0.2 - - - -
411B LYS* 1.3 77.4 - - - +
413B VAL* 1.3 70.2 + - - +
414B TRP* 2.9 18.1 - - - +
1002B NAG 3.3 23.0 + - - +
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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