Contacts of the helix formed by residues 401 - 408 (chain F) in PDB entry 3SWD
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 ARG 401 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46F LYS* 4.7 7.4 + - - +
399F TYR 3.3 5.5 + - - -
400F GLU* 1.3 102.0 + - + +
402F ILE* 1.3 64.9 + - - +
403F GLU* 3.2 13.2 - - - +
404F ASP* 3.1 51.7 + - - +
405F LYS* 3.4 24.6 + - - +
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Residues in contact with ILE 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F PHE* 4.0 26.9 - - + -
234F GLU* 6.1 0.9 - - - +
237F THR* 5.1 6.3 - - + -
238F PHE* 4.3 16.8 - - + -
374F ALA* 4.4 18.8 - - + -
377F VAL* 5.2 6.7 - - + -
378F LEU* 5.1 3.8 - - + -
395F ILE* 4.1 13.9 - - + -
396F ASP* 6.0 0.9 - - - +
399F TYR* 4.0 39.7 + - + +
400F GLU 3.3 3.4 + - - -
401F ARG* 1.3 74.6 - - - +
403F GLU* 1.3 68.4 + - - +
405F LYS* 3.5 5.5 + - - +
406F LEU* 3.1 42.5 + - + +
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Residues in contact with GLU 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F PHE* 3.6 24.2 - - + -
396F ASP* 5.4 0.3 - - - +
401F ARG* 3.7 10.3 - - - +
402F ILE* 1.3 84.7 + - - +
404F ASP* 1.3 69.8 + - - +
406F LEU* 3.5 0.7 + - - -
407F ARG* 2.9 46.1 + - - +
413F ILE* 3.7 27.9 - - + +
415F ARG* 2.8 49.1 + - + +
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Residues in contact with ASP 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401F ARG* 3.1 54.0 + - - +
402F ILE 3.3 0.6 - - - -
403F GLU* 1.3 82.4 - - - +
405F LYS* 1.3 63.2 + - + +
407F ARG* 2.9 31.9 + - - +
408F ALA* 3.0 24.1 + - - +
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Residues in contact with LYS 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLU 5.2 0.9 - - - +
16F VAL* 3.9 23.9 - - + +
17F THR 3.3 19.3 + - - +
19F SER* 2.8 29.2 + - - -
234F GLU* 3.1 24.8 + - - +
238F PHE* 3.7 22.7 - - + -
400F GLU* 3.7 22.7 + - - +
401F ARG* 3.4 17.3 + - - +
402F ILE* 4.2 2.5 - - - +
403F GLU 3.4 0.2 - - - -
404F ASP* 1.3 79.1 - - + +
406F LEU* 1.3 59.9 + - - +
408F ALA* 3.4 15.0 + - - +
409F LEU* 3.4 18.9 + - - +
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Residues in contact with LEU 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 4.1 25.7 - - + +
238F PHE* 3.8 24.7 - - + -
241F ALA* 4.7 1.3 - - + -
377F VAL* 3.6 30.1 - - + -
378F LEU* 4.5 16.2 - - + -
381F CYS* 4.5 7.9 - - - -
402F ILE* 3.1 34.3 + - + +
403F GLU 4.0 2.9 - - - +
405F LYS* 1.3 72.1 - - - +
407F ARG* 1.3 61.0 + - - +
409F LEU* 2.9 23.3 + - + +
410F GLY 3.3 0.5 + - - -
411F ALA* 3.1 27.8 + - + +
413F ILE* 4.5 9.2 - - + -
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Residues in contact with ARG 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F GLU* 2.9 31.4 + - - +
404F ASP* 2.9 32.7 + - - +
406F LEU* 1.3 70.6 - - - +
408F ALA* 1.3 55.9 - - - +
409F LEU 2.9 4.7 - - - -
410F GLY* 2.9 19.9 + - - -
411F ALA* 3.8 22.3 + - - +
413F ILE* 2.8 40.4 + - + +
414F GLU* 4.4 7.1 - - - +
415F ARG 5.2 1.4 - - - +
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Residues in contact with ALA 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLN 4.2 4.2 - - - +
14F GLY* 5.2 0.7 - - - -
15F GLU 4.7 12.7 + - - +
404F ASP 3.0 12.7 + - - +
405F LYS* 3.6 12.3 - - - +
406F LEU 3.2 0.6 - - - -
407F ARG* 1.3 73.6 - - - +
409F LEU* 1.3 63.4 + - - +
410F GLY 3.4 0.2 - - - -
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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