Contacts of the helix formed by residues 394 - 406 (chain B) in PDB entry 4F5G
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 394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.7 27.0 - - + +
389B GLY 3.1 24.2 + - - -
391B THR* 2.8 41.7 + - - +
393B ASP* 1.3 75.5 - - - +
395B MET* 1.3 65.2 + - - +
396B ALA 3.4 1.6 - - - -
397B PRO* 3.4 10.5 - - + +
398B LEU* 3.2 38.2 + - - +
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Residues in contact with MET 395 (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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331B MET* 3.7 17.3 - - - +
334B LEU* 3.8 26.0 - - + +
335B PHE* 3.7 45.1 - - - +
338B THR* 3.6 25.6 - - - +
390B MET* 3.6 29.6 - - + +
391B THR 3.0 15.8 + - - +
392B PRO 4.1 4.9 - - - +
393B ASP 3.4 1.8 - - - -
394B ASN* 1.3 79.5 - - - +
396B ALA* 1.3 58.1 + - - +
398B LEU* 3.4 6.3 + - - +
399B CYS* 2.9 33.4 + - - -
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Residues in contact with ALA 396 (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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338B THR* 4.0 15.7 - - + +
341B GLU* 6.6 0.2 - - - -
342B LYS* 4.3 14.6 - - - +
392B PRO 4.8 2.4 + - - +
393B ASP 4.9 0.4 + - - -
395B MET* 1.3 78.6 - - - +
397B PRO* 1.3 65.7 - - + +
399B CYS* 3.2 1.9 + - - +
400B GLU* 2.8 37.9 + - - +
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Residues in contact with PRO 397 (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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37B GLY 6.0 2.5 - - - +
377B VAL* 5.6 0.4 - - - -
393B ASP 4.1 8.7 - - - +
394B ASN* 3.4 22.7 - - + +
396B ALA* 1.3 94.6 - - + +
398B LEU* 1.3 56.3 + - - +
400B GLU* 3.3 11.9 + - + +
401B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 398 (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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39B VAL* 4.2 17.2 - - + +
41B LEU* 4.4 11.0 - - + -
335B PHE* 3.8 31.2 - - + -
377B VAL* 4.3 21.2 - - + +
390B MET* 4.0 18.6 - - + -
394B ASN* 3.2 46.7 + - - +
395B MET* 3.5 8.1 - - - +
397B PRO* 1.3 76.7 - - - +
399B CYS* 1.3 64.4 + - - +
401B ALA* 3.3 8.0 + - - +
402B ILE* 2.9 37.6 + - + +
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Residues in contact with CYS 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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335B PHE* 3.7 35.4 - - - -
338B THR* 3.6 33.7 - - + -
339B LEU* 3.9 17.4 - - + +
342B LYS* 4.1 7.4 - - + -
395B MET* 2.9 29.5 + - - +
396B ALA 3.8 0.4 - - - +
398B LEU* 1.3 75.1 - - - +
400B GLU* 1.3 59.2 + - - +
402B ILE* 3.2 2.7 + - - +
403B VAL* 2.9 34.0 + - - +
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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
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342B LYS* 2.5 46.1 + - - +
375B PHE* 5.6 0.4 - - - -
396B ALA* 2.8 29.9 + - - +
397B PRO* 3.6 9.6 - - + +
399B CYS* 1.3 76.6 - - - +
401B ALA* 1.3 62.2 + - - +
403B VAL* 3.4 3.9 + - - +
404B ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 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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371B LEU* 3.7 10.1 - - + -
375B PHE* 3.5 45.7 - - + -
377B VAL* 4.0 7.2 - - + -
397B PRO 2.9 14.1 + - - +
398B LEU 3.4 9.2 - - - +
400B GLU* 1.3 77.4 - - - +
402B ILE* 1.3 62.3 + - - +
404B ALA* 3.2 10.7 + - - +
405B VAL* 3.3 20.1 + - - +
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Residues in contact with ILE 402 (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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41B LEU* 5.2 8.1 - - + -
335B PHE* 3.5 35.7 - - + -
339B LEU* 3.9 14.8 - - + -
348B PHE* 4.8 7.0 - - + -
361B SER* 6.2 1.1 - - - -
363B LEU* 4.4 17.7 - - + -
371B LEU* 4.0 24.7 - - + -
377B VAL* 5.4 2.7 - - + -
398B LEU* 2.9 28.5 + - + +
399B CYS* 3.7 5.6 - - - +
401B ALA* 1.3 75.7 - - - +
403B VAL* 1.3 62.9 + - - +
405B VAL* 3.0 15.1 + - - +
406B LEU* 3.2 30.4 + - + +
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Residues in contact with VAL 403 (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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339B LEU* 3.9 10.3 - - + +
342B LYS* 3.3 33.2 - - + +
343B GLY 3.8 13.7 - - - +
344B ALA* 3.7 28.5 - - + +
345B ASN* 5.4 1.0 + - - +
399B CYS 2.9 20.6 + - - +
400B GLU* 3.7 4.9 - - - +
402B ILE* 1.3 75.5 - - - +
404B ALA* 1.3 63.3 + - - +
405B VAL 3.2 1.0 + - - -
406B LEU* 3.3 23.2 + - + +
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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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370B ARG* 3.4 18.8 + - - +
375B PHE* 3.7 24.5 - - + -
400B GLU 3.0 17.9 + - - +
401B ALA 3.4 6.3 - - - +
402B ILE 3.1 0.4 - - - -
403B VAL* 1.3 79.6 - - - +
405B VAL* 1.3 59.0 + - - +
406B LEU* 4.6 2.4 - - - +
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Residues in contact with VAL 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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363B LEU* 4.4 7.0 - - + -
367B GLN* 3.0 43.5 + - + +
370B ARG* 3.6 42.8 + - + +
371B LEU* 4.0 24.0 - - + -
375B PHE* 3.8 12.1 - - + -
401B ALA 3.3 13.2 - - - +
402B ILE* 3.0 17.0 + - - +
404B ALA* 1.3 77.6 - - - +
406B LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 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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344B ALA* 4.1 16.8 - - + -
345B ASN* 3.8 41.1 + - - +
346B ARG* 3.7 23.1 - - + +
348B PHE* 4.0 25.4 - - + -
363B LEU* 3.7 29.6 - - + -
367B GLN* 3.6 13.3 + - - +
402B ILE* 3.2 18.1 + - + +
403B VAL* 3.3 19.4 + - - +
404B ALA 4.6 2.6 - - - +
405B VAL* 1.3 83.2 - - - +
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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