Contacts of the helix formed by residues 401 - 408 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K LYS* 4.9 5.7 + - - +
399K TYR 3.4 4.6 + - - -
400K GLU* 1.3 99.0 + - + +
402K ILE* 1.3 66.4 + - - +
403K GLU* 3.3 10.5 - - - +
404K ASP* 3.1 47.7 + - - +
405K LYS* 3.3 22.4 + - + +
415K ARG* 6.2 0.2 - - - +
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Residues in contact with ILE 402 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K PHE* 4.0 25.8 - - + -
234K GLU* 6.1 0.2 - - - -
237K THR* 5.2 2.0 - - + -
238K PHE* 4.3 15.0 - - + -
374K ALA* 4.7 15.3 - - + -
377K VAL* 4.7 9.6 - - + -
378K LEU* 4.8 6.3 - - + -
395K ILE* 4.2 18.2 - - + -
396K ASP* 5.6 2.5 - - - +
399K TYR* 4.1 35.2 + - + +
400K GLU 3.2 5.2 + - - -
401K ARG* 1.3 73.3 - - - +
403K GLU* 1.3 80.1 + - + +
405K LYS* 3.0 8.5 + - - +
406K LEU* 2.9 42.9 + - + +
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Residues in contact with GLU 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K PHE* 3.0 21.6 - - + -
401K ARG* 4.6 7.1 - - - +
402K ILE* 1.3 87.8 + - - +
404K ASP* 1.3 74.0 + - - +
406K LEU* 3.6 1.5 + - - +
407K ARG* 3.1 39.3 + - - +
413K ILE* 3.3 39.0 - - + +
415K ARG* 2.9 47.6 + - + +
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Residues in contact with ASP 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K ARG* 3.1 49.4 + - - +
402K ILE 3.2 0.8 - - - -
403K GLU* 1.3 85.2 - - - +
405K LYS* 1.3 66.0 - - + +
407K ARG* 2.9 37.1 + - - +
408K ALA* 3.1 14.0 + - - +
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Residues in contact with LYS 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K VAL* 3.8 22.1 - - + +
17K THR 3.1 21.6 + - - +
18K ILE* 4.5 0.2 - - - +
19K SER* 3.0 23.6 + - - -
234K GLU* 2.9 28.4 + - - +
238K PHE* 3.8 17.7 - - + -
400K GLU* 3.6 20.2 - - - +
401K ARG* 3.3 19.5 + - + +
402K ILE* 3.0 7.9 + - - +
404K ASP* 1.3 78.1 - - + +
406K LEU* 1.3 60.9 + - - +
408K ALA* 3.6 11.5 + - - +
409K LEU* 3.4 20.9 - - - +
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Residues in contact with LEU 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 4.5 21.9 - - + +
238K PHE* 3.9 26.0 - - + -
241K ALA* 4.8 4.3 - - + -
377K VAL* 3.4 32.8 - - + -
378K LEU* 4.6 9.6 - - + -
381K CYS* 4.5 11.7 - - - -
402K ILE* 2.9 29.7 + - + +
403K GLU 4.0 4.0 - - - +
405K LYS* 1.3 74.0 - - - +
407K ARG* 1.3 54.3 + - - +
409K LEU* 2.8 32.7 + - + +
411K ALA* 2.8 26.5 - - + +
413K ILE* 4.3 10.8 - - + -
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Residues in contact with ARG 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403K GLU* 3.1 23.4 + - - +
404K ASP* 2.9 33.0 + - - +
406K LEU* 1.3 71.0 - - - +
408K ALA* 1.3 57.9 + - - +
409K LEU 2.8 11.1 + - - -
410K GLY* 3.1 11.6 + - - -
411K ALA* 3.1 27.5 + - + +
412K ASN* 5.6 0.2 - - - +
413K ILE* 2.6 46.8 + - + +
414K GLU* 4.7 1.6 - - - +
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Residues in contact with ALA 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K GLN 3.9 3.8 - - - +
14K GLY* 4.8 1.9 - - - -
15K GLU 5.2 7.9 + - - +
404K ASP 3.1 10.9 + - - +
405K LYS* 4.0 11.2 - - - +
406K LEU 3.2 0.6 - - - -
407K ARG* 1.3 73.4 - - - +
409K LEU* 1.3 67.8 + - + +
410K GLY 3.6 0.7 - - - -
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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