Contacts of the helix formed by residues 404 - 414 (chain B) in PDB entry 4FGU
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 HIS 404 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345B ILE* 3.5 40.1 - - + +
346B GLU* 3.7 28.7 - - + +
349B VAL* 4.4 25.5 - - + +
367B LEU* 6.0 1.6 - - + -
387B ARG* 5.3 5.4 + - - +
400B TYR* 3.6 30.5 + + - -
401B ALA* 3.0 13.4 + - - +
402B LEU 3.0 1.2 - - - -
403B ARG* 1.3 83.4 - - - +
405B LEU* 1.3 64.7 + - + +
406B TYR* 3.3 8.7 - + - -
407B VAL* 3.4 26.3 - - + +
408B LEU* 4.2 6.6 + - - +
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Residues in contact with LEU 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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150B SER* 3.4 27.1 - - - +
151B THR* 4.9 1.6 - - - -
153B ILE* 3.8 24.0 - - + -
379B TYR* 4.1 18.8 + - - +
384B LEU* 4.7 6.1 - - + -
387B ARG* 4.0 21.5 - - + +
393B TRP* 4.4 16.8 - - + +
401B ALA* 3.6 15.7 - - + +
402B LEU* 3.2 14.4 + - + +
404B HIS* 1.3 78.3 - - - +
406B TYR* 1.3 60.7 + - - +
407B VAL 3.0 6.3 + - - -
408B LEU* 3.4 35.6 + - + +
409B VAL* 3.6 11.6 + - - +
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Residues in contact with TYR 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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150B SER* 5.2 0.2 + - - -
151B THR* 4.3 9.6 + - + +
190B GLU* 4.5 1.8 + - - +
366B LEU 5.4 0.2 - - - -
367B LEU* 2.8 30.9 + - - +
368B SER 4.6 4.3 - - - -
369B GLU 3.9 13.2 - - - -
370B ARG* 3.4 57.2 - - + +
402B LEU 4.5 1.6 + - - -
403B ARG* 3.2 30.1 - - + -
404B HIS* 3.3 5.1 - + - -
405B LEU* 1.3 78.2 - - - +
407B VAL* 1.3 74.8 + - + +
409B VAL* 3.1 20.4 - - + +
410B ASN* 2.6 33.8 + - - -
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Residues in contact with VAL 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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349B VAL* 3.9 28.9 - - + -
353B VAL* 4.0 15.0 - - + -
366B LEU 3.7 15.9 - - - +
367B LEU* 4.1 11.4 - - + -
404B HIS* 3.4 20.6 - - + +
405B LEU 3.0 0.6 - - - -
406B TYR* 1.3 101.0 - - + +
408B LEU* 1.3 60.0 + - + +
409B VAL 3.2 0.3 + - - -
410B ASN* 3.0 12.0 - - - +
411B LEU* 2.8 44.0 + - + +
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Residues in contact with LEU 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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349B VAL* 5.8 3.6 - - + -
352B ILE* 6.5 0.2 - - + -
379B TYR* 3.7 33.7 - - + -
383B LEU* 4.7 7.2 - - + +
384B LEU* 4.6 3.8 - - - -
387B ARG* 3.7 26.7 - - + +
404B HIS 4.3 4.5 - - - +
405B LEU* 3.4 33.4 + - + +
407B VAL* 1.3 80.6 - - + +
409B VAL* 1.3 52.9 + - - +
411B LEU* 3.1 18.7 + - + +
412B CYS* 2.7 37.2 + - - +
421B ILE* 5.4 2.1 - - + +
425B MET* 3.7 27.6 - - + -
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Residues in contact with VAL 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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151B THR* 4.3 14.4 - - + -
371B ALA 4.4 11.9 - - - +
372B PRO* 4.9 0.2 - - + -
373B LEU* 3.2 42.8 - - + +
379B TYR* 3.7 26.2 - - + -
405B LEU 3.6 6.2 + - - +
406B TYR* 3.1 31.0 - - + +
408B LEU* 1.3 79.6 - - - +
410B ASN* 1.3 52.0 + - - +
412B CYS* 3.0 4.0 + - + +
413B GLU* 2.6 38.6 + - - +
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Residues in contact with ASN 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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366B LEU* 3.3 26.9 - - - +
369B GLU* 2.5 39.5 + - + +
370B ARG* 3.7 7.9 - - - +
371B ALA* 3.3 28.1 - - + +
406B TYR* 2.6 26.5 + - - -
407B VAL* 3.0 14.9 - - - +
409B VAL* 1.3 76.6 - - - +
411B LEU* 1.3 58.5 + - - +
412B CYS 3.3 0.2 - - - -
413B GLU* 4.1 4.5 - - - +
414B LYS* 3.3 30.6 + - + +
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Residues in contact with LEU 411 (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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352B ILE* 4.5 14.6 - - + -
353B VAL* 3.9 22.7 - - + -
356B LEU* 3.7 25.1 - - + -
366B LEU* 3.6 29.6 - - + -
407B VAL* 2.8 24.2 + - + +
408B LEU* 3.1 20.2 + - + +
410B ASN* 1.3 77.8 - - - +
412B CYS* 1.3 57.9 + - - +
414B LYS 3.2 12.1 - - - +
416B TYR* 3.4 17.4 - - - +
421B ILE* 3.9 29.9 - - + +
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Residues in contact with CYS 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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378B CYS* 2.0 54.8 - - + -
379B TYR* 3.6 12.6 - - + -
383B LEU* 3.2 27.8 - - - -
408B LEU 2.7 12.4 + - - +
409B VAL* 3.0 4.5 + - + +
411B LEU* 1.3 77.5 - - - +
413B GLU* 1.3 63.3 + - - +
414B LYS 2.8 15.6 - - - +
415B PRO* 4.0 2.1 - - - +
416B TYR* 3.9 6.0 + - - +
421B ILE* 3.8 8.7 - - - -
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Residues in contact with GLU 413 (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 ALA* 4.4 1.8 - - + -
372B PRO* 2.3 45.9 - - + +
373B LEU* 4.0 3.8 + - - -
374B THR* 2.4 39.1 + - - -
375B GLY* 3.9 9.1 + - - -
409B VAL* 2.6 22.0 + - - +
410B ASN* 4.3 3.8 - - - -
412B CYS* 1.3 71.1 - - - +
414B LYS* 1.3 63.4 + - - +
415B PRO* 3.3 8.3 - - - +
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Residues in contact with LYS 414 (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 GLU* 5.5 6.0 - - + +
365B GLN* 4.1 14.9 + - - -
366B LEU* 3.7 14.8 - - + -
369B GLU* 3.9 23.2 + - - +
410B ASN* 3.3 22.3 + - + +
411B LEU 3.2 3.7 - - - +
412B CYS 2.8 7.4 - - - +
413B GLU* 1.3 75.3 - - - +
415B PRO* 1.3 64.2 - - + -
416B TYR* 2.7 48.4 + - + -
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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