Contacts of the helix formed by residues 401 - 411 (chain A) in PDB entry 1FBV
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 CYS 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381A CYS* 3.1 15.2 - - + +
384A CYS* 3.5 6.3 - - - -
387A ASN* 3.7 12.3 - - + -
388A ASP 3.4 24.9 - - - +
390A ASP* 3.7 1.3 - - - +
391A VAL* 4.3 0.2 - - - -
400A MET* 1.3 76.7 - - - +
402A THR* 1.3 67.1 + - - +
403A SER* 3.5 14.4 - - - +
404A CYS* 3.0 26.4 + - - +
405A LEU 3.2 9.5 + - - -
1001A ZN 2.3 33.4 - - - -
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Residues in contact with THR 402 (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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390A ASP* 2.6 38.7 + - - +
391A VAL* 3.2 18.9 - - - +
401A CYS* 1.3 71.4 - - + +
403A SER* 1.3 66.5 + - - +
405A LEU* 3.1 7.9 + - - +
406A THR* 2.6 43.7 + - + +
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Residues in contact with SER 403 (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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387A ASN* 4.0 16.0 + - - -
401A CYS* 3.1 14.3 - - - -
402A THR* 1.3 86.6 - - - +
404A CYS* 1.3 56.9 + - - +
406A THR* 3.1 12.1 - - - +
407A SER* 2.9 26.7 + - - -
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Residues in contact with CYS 404 (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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383A ILE* 3.9 8.5 - - + -
384A CYS* 3.3 25.8 - - - -
387A ASN* 5.3 0.2 - - - -
400A MET* 3.9 9.9 - - + -
401A CYS* 3.0 12.4 + - - +
403A SER* 1.3 73.9 - - - +
405A LEU* 1.3 59.9 + - - +
406A THR 3.0 1.1 - - - -
407A SER* 2.5 29.2 + - - -
408A TRP* 2.7 14.3 + - - +
1001A ZN 2.3 36.3 - - - -
1063C PHE* 3.8 24.5 - - + -
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Residues in contact with LEU 405 (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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391A VAL* 4.1 9.9 - - + -
393A ILE* 3.1 34.8 - - + -
400A MET* 3.0 27.0 - - + +
401A CYS 3.2 2.9 + - - +
402A THR* 3.1 12.3 + - - +
404A CYS* 1.3 74.8 - - - +
406A THR* 1.3 64.4 + - - +
408A TRP* 3.2 5.9 + - + +
409A GLN* 2.9 55.1 + - + +
417A PRO* 5.1 4.3 - - + -
423A ILE* 5.3 3.8 - - + -
426A THR* 3.6 22.4 - - + -
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Residues in contact with THR 406 (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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402A THR* 2.6 40.6 + - + +
403A SER* 3.1 23.6 - - - +
405A LEU* 1.3 75.5 - - - +
407A SER* 1.3 61.6 + - - +
408A TRP 3.2 0.2 + - - -
409A GLN* 3.4 10.3 + - - +
410A GLU* 3.1 36.4 + - - +
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Residues in contact with SER 407 (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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403A SER 2.9 19.6 + - - -
404A CYS* 2.5 14.5 + - - -
406A THR* 1.3 73.9 + - - +
408A TRP* 1.3 59.9 + - - +
410A GLU* 3.9 6.2 + - - +
411A SER* 3.6 17.2 + - - -
1063C PHE* 3.7 32.1 - - - -
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Residues in contact with TRP 408 (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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404A CYS 2.7 12.6 + - - +
405A LEU* 3.8 7.0 - - + +
407A SER* 1.3 72.5 - - - +
409A GLN* 1.3 70.0 + - + +
411A SER* 2.6 30.0 + - - -
412A GLU 3.1 4.7 + - - -
413A GLY* 3.2 31.3 + - - -
414A GLN 2.9 20.4 - - - -
415A GLY 2.5 30.5 - - - -
416A CYS 3.1 21.5 - - - -
417A PRO* 3.2 24.5 - - + -
420A ARG* 3.8 17.5 - - + -
1063C PHE* 3.6 42.2 + + + -
1095C TRP* 4.3 5.4 - - - -
1097C PRO* 3.6 24.1 - - + +
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Residues in contact with GLN 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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405A LEU* 2.9 39.8 + - + +
406A THR* 4.0 9.0 - - - +
408A TRP* 1.3 79.7 - - + +
410A GLU* 1.3 63.1 + - - +
412A GLU* 2.6 28.9 + - - +
413A GLY 4.2 9.9 - - - +
415A GLY 5.7 0.4 - - - +
423A ILE* 3.3 33.3 - - + +
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Residues in contact with GLU 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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406A THR* 3.1 32.3 + - - +
407A SER* 4.1 6.7 - - - +
409A GLN* 1.3 84.0 - - - +
411A SER* 1.3 57.8 + - - +
412A GLU* 3.1 6.2 + - - +
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Residues in contact with SER 411 (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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407A SER 3.6 10.1 + - - -
408A TRP* 2.6 35.0 + - - -
410A GLU* 1.3 76.2 - - - +
412A GLU* 1.3 70.5 + - - +
413A GLY* 4.2 0.5 + - - -
1060C GLU* 6.4 1.6 - - - -
1063C PHE* 4.3 14.8 + - - +
1064C LYS* 5.8 9.9 - - - -
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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