Contacts of the helix formed by residues 396 - 412 (chain A) in PDB entry 4S15
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 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A PHE 5.3 1.0 + - - -
392A LYS 4.9 0.4 + - - -
394A LEU* 3.3 21.7 - - - +
395A GLY* 1.3 79.3 - - - +
397A GLU* 1.3 64.7 + - - +
398A ASP* 3.1 15.0 - - - +
399A PHE* 3.0 26.4 + - + -
400A ILE* 3.0 16.4 + - - +
483A ARG* 5.2 2.2 - - - +
487A LYS* 3.1 39.7 - - + +
601A 4D8 4.7 2.5 - - - -
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Residues in contact with GLU 397 (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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395A GLY 3.9 1.2 - - - -
396A CYS* 1.3 74.8 - - - +
398A ASP* 1.3 61.7 + - + +
400A ILE* 3.8 8.7 - - - +
401A SER* 2.9 31.2 + - - -
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A CYS* 3.5 17.7 - - - +
397A GLU* 1.3 77.6 + - + +
399A PHE* 1.3 71.3 + - - -
401A SER* 3.4 6.4 + - - -
402A PHE* 3.0 23.2 + - - +
483A ARG* 3.1 32.0 + - - +
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Residues in contact with PHE 399 (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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365A PHE* 4.6 8.7 - + - -
396A CYS* 3.0 20.3 + - + +
398A ASP* 1.3 79.9 - - - +
400A ILE* 1.3 71.6 + - + +
402A PHE* 3.1 7.7 + - + +
403A VAL* 3.0 37.5 + - + +
480A LEU* 3.6 29.4 - - + -
483A ARG* 3.6 54.7 - - + +
484A HIS* 4.2 17.0 - + + -
487A LYS* 3.8 20.6 - - + -
601A 4D8 3.7 26.7 - - + -
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Residues in contact with ILE 400 (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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388A PRO* 4.0 22.4 - - + +
391A PHE* 4.0 31.4 - - + +
394A LEU* 4.0 16.2 - - + -
396A CYS* 3.0 21.0 + - - +
397A GLU* 3.9 8.5 - - - +
399A PHE* 1.3 81.1 - - + +
401A SER* 1.3 62.5 + - - +
403A VAL* 3.1 5.8 + - - +
404A PHE* 2.9 47.2 + - + -
601A 4D8 4.2 25.8 - - + -
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PRO* 5.6 4.9 - - - +
397A GLU 2.9 20.7 + - - -
398A ASP* 3.6 8.3 - - - -
399A PHE 3.3 0.2 - - - -
400A ILE* 1.3 76.0 - - - +
402A PHE* 1.3 56.8 + - - +
404A PHE* 3.4 7.0 + - - +
405A GLU* 2.9 43.4 + - - +
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Residues in contact with PHE 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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398A ASP 3.0 13.6 + - - +
399A PHE* 3.1 11.9 + + - +
401A SER* 1.3 73.8 - - - +
403A VAL* 1.3 65.5 + - - +
405A GLU* 3.3 21.8 + - + -
406A PHE* 3.1 22.6 + - - +
476A THR* 3.6 32.1 - - + -
479A ALA* 4.2 21.8 - - + -
480A LEU* 3.5 27.9 - - + +
483A ARG* 5.1 14.8 - - + +
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Residues in contact with VAL 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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365A PHE* 4.1 13.9 - - + -
368A MET* 3.5 32.5 - - + +
399A PHE* 3.0 41.3 + - + +
400A ILE* 3.1 8.5 + - - +
402A PHE* 1.3 75.9 - - - +
404A PHE* 1.3 69.7 + - + +
406A PHE* 3.2 3.3 + - - +
407A GLY 3.0 18.4 + - - -
480A LEU* 3.7 22.2 - - + -
601A 4D8 3.7 24.0 - - + -
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Residues in contact with PHE 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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372A PHE* 3.3 21.7 - + - -
377A ASN* 3.5 46.4 - - - +
378A THR* 4.0 5.2 - - - -
379A VAL* 3.6 25.6 - - + -
386A ALA 3.5 15.7 - - - -
387A SER 3.8 2.2 - - - -
388A PRO* 3.6 26.2 - - + -
391A PHE* 3.9 12.1 - + - -
400A ILE* 2.9 41.8 + - + +
401A SER* 3.8 6.3 - - - +
403A VAL* 1.3 85.9 - - + +
405A GLU* 1.3 57.5 + - - +
408A LYS* 2.8 28.8 + - - +
601A 4D8 5.4 2.9 - - + -
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Residues in contact with GLU 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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401A SER* 2.9 31.0 + - - +
402A PHE* 3.4 25.7 - - + +
403A VAL 3.2 0.2 - - - -
404A PHE* 1.3 77.6 - - - +
406A PHE* 1.3 57.7 + - - +
408A LYS* 3.5 5.5 + - - +
409A SER* 3.0 30.3 + - - -
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Residues in contact with PHE 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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365A PHE* 3.6 26.2 - - + -
366A ILE* 4.7 0.7 - - + -
368A MET* 4.3 5.4 - - + -
369A CYS* 6.2 0.2 - - + -
402A PHE* 3.1 8.4 + - - +
403A VAL 3.6 6.5 - - - +
405A GLU* 1.3 72.9 - - - +
407A GLY* 1.3 69.7 + - - +
409A SER* 3.4 5.3 + - - -
410A LEU* 3.0 50.1 + - + +
423A PHE* 5.3 0.4 - + - -
473A LYS* 3.9 33.2 - - + -
476A THR* 3.8 23.6 - - + -
477A LEU* 3.4 41.5 - - + -
480A LEU* 3.7 25.4 - - + -
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Residues in contact with GLY 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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365A PHE 5.8 0.2 - - - -
368A MET* 3.7 20.6 - - - +
369A CYS* 4.4 5.3 - - - +
372A PHE* 3.8 18.2 - - - -
403A VAL 3.0 10.3 + - - -
404A PHE 3.3 2.9 + - - -
406A PHE* 1.3 78.7 - - - +
408A LYS* 1.3 56.3 + - - +
410A LEU* 4.1 2.1 - - - +
411A CYS* 2.8 34.3 + - - +
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Residues in contact with LYS 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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372A PHE* 3.4 16.2 - - + -
374A SER* 3.3 34.3 + - - +
375A GLN 5.6 1.8 + - - -
377A ASN* 4.4 15.7 - - - +
404A PHE 2.8 20.8 + - - +
405A GLU* 3.9 6.3 - - - +
407A GLY* 1.3 72.7 - - - +
409A SER* 1.3 63.5 + - - +
412A SER* 3.1 28.6 + - - -
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Residues in contact with SER 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 GLU 3.0 19.3 + - - -
406A PHE* 3.7 7.4 - - - -
408A LYS* 1.3 77.4 - - - +
410A LEU* 1.3 60.3 + - - +
412A SER* 3.0 20.6 + - - -
413A MET* 3.3 12.6 - - - +
469A LYS* 4.0 7.8 + - - -
473A LYS* 3.0 29.6 + - - -
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Residues in contact with LEU 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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366A ILE* 4.1 25.8 - - + +
369A CYS* 3.9 28.9 - - + +
406A PHE* 3.0 45.3 + - + +
407A GLY* 4.9 0.2 - - - -
409A SER* 1.3 74.3 - - - +
411A CYS* 1.3 64.7 + - - +
413A MET* 3.0 30.5 + - - +
414A HIS 4.0 2.1 + - - -
415A LEU* 3.9 14.3 + - + +
423A PHE* 4.5 6.1 - - + -
470A LEU* 3.8 29.4 - - + -
473A LYS* 4.2 10.5 - - + +
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Residues in contact with CYS 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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292A ARG* 5.6 4.6 + - - +
369A CYS* 3.7 25.5 - - + +
372A PHE* 3.2 31.6 - - + -
374A SER* 3.9 21.5 + - - -
375A GLN* 5.3 1.3 - - - -
407A GLY 2.8 19.6 + - - +
408A LYS 4.2 2.5 - - - +
410A LEU* 1.3 77.3 - - - +
412A SER* 1.3 59.7 + - - +
413A MET 3.2 0.4 - - - -
414A HIS* 3.3 22.5 + - - +
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Residues in contact with SER 412 (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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374A SER* 4.5 12.3 - - - -
408A LYS* 3.1 17.8 + - - -
409A SER* 3.0 17.0 + - - -
410A LEU 3.1 0.4 - - - -
411A CYS* 1.3 74.1 - - - +
413A MET* 1.3 56.9 + - - +
414A HIS* 3.2 26.6 + - - -
469A LYS* 5.9 0.3 + - - -
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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