Contacts of the helix formed by residues 401 - 408 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46I LYS* 4.7 7.0 + - - +
399I TYR 3.3 5.5 + - - -
400I GLU* 1.3 101.6 + - + +
402I ILE* 1.3 65.8 + - - +
403I GLU* 3.2 13.2 - - - +
404I ASP* 3.0 51.7 + - - +
405I LYS* 3.4 22.9 + - - +
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Residues in contact with ILE 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I PHE* 4.0 26.9 - - + -
234I GLU* 6.0 0.7 - - - +
237I THR* 5.1 6.3 - - + -
238I PHE* 4.3 17.5 - - + -
374I ALA* 4.4 19.3 - - + -
377I VAL* 5.2 6.1 - - + -
378I LEU* 5.1 4.3 - - + -
395I ILE* 4.1 14.4 - - + -
396I ASP* 6.0 0.7 - - - +
399I TYR* 4.0 38.2 + - + -
400I GLU 3.3 3.4 + - - -
401I ARG* 1.3 75.5 - - - +
403I GLU* 1.3 68.1 + - - +
405I LYS* 3.5 4.8 + - - +
406I LEU* 3.0 43.9 + - + +
413I ILE* 5.6 0.2 - - + -
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Residues in contact with GLU 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I PHE* 3.7 23.0 - - + -
396I ASP* 5.4 0.3 - - - +
401I ARG* 3.7 10.4 - - - -
402I ILE* 1.3 85.2 + - - +
404I ASP* 1.3 70.1 + - - +
407I ARG* 2.9 46.2 + - - +
413I ILE* 3.7 28.4 - - + +
415I ARG* 2.8 49.1 + - + +
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Residues in contact with ASP 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401I ARG* 3.0 54.9 + - - +
403I GLU* 1.3 83.0 - - - +
405I LYS* 1.3 63.5 + - + +
407I ARG* 2.8 30.9 + - - +
408I ALA* 3.0 23.4 + - - +
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Residues in contact with LYS 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I GLU 5.2 0.2 - - - +
16I VAL* 3.8 24.9 - - + +
17I THR 3.3 19.0 + - - +
19I SER* 2.8 28.4 + - - -
234I GLU* 3.1 26.1 + - - +
238I PHE* 3.7 22.4 - - + -
400I GLU* 3.7 21.7 + - - +
401I ARG* 3.4 18.2 + - - +
402I ILE* 3.5 2.7 + - - +
403I GLU 3.4 0.2 - - - -
404I ASP* 1.3 77.4 - - + +
406I LEU* 1.3 60.8 + - - +
408I ALA* 3.3 14.9 + - - +
409I LEU* 3.4 18.5 + - - +
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Residues in contact with LEU 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I LEU* 4.1 26.2 - - + +
238I PHE* 3.8 25.8 - - + -
241I ALA* 4.7 1.6 - - + -
377I VAL* 3.6 30.7 - - + -
378I LEU* 4.6 14.6 - - + -
381I CYS* 4.4 8.5 - - - -
402I ILE* 3.0 32.9 + - + +
403I GLU 4.1 2.2 - - - +
405I LYS* 1.3 72.1 - - - +
407I ARG* 1.3 60.9 + - - +
409I LEU* 2.9 22.6 + - + +
410I GLY 3.3 0.3 + - - -
411I ALA* 3.0 29.5 + - + +
413I ILE* 4.4 11.4 - - + -
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Residues in contact with ARG 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403I GLU* 2.9 31.0 + - - +
404I ASP* 2.8 32.9 + - - +
406I LEU* 1.3 72.9 - - - +
408I ALA* 1.3 55.6 + - - +
409I LEU 3.0 5.4 - - - -
410I GLY* 3.0 19.9 + - - -
411I ALA* 3.8 20.2 + - - +
412I ASN* 6.0 0.2 - - - +
413I ILE* 2.7 40.6 + - + +
414I GLU* 4.4 6.3 - - - +
415I ARG 5.2 1.2 - - - +
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Residues in contact with ALA 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I GLN 4.2 4.5 - - - +
14I GLY* 5.3 0.5 - - - -
15I GLU 4.8 12.9 + - - +
404I ASP 3.0 13.2 + - - +
405I LYS* 3.6 12.8 - - - +
406I LEU 3.2 0.4 - - - -
407I ARG* 1.3 74.7 - - - +
409I LEU* 1.3 62.0 + - - +
410I GLY 3.4 0.6 + - - -
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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