Contacts of the helix formed by residues 394 - 405 (chain A) in PDB entry 5I4E
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A MET* 4.0 26.3 + - + +
392A PRO 5.1 3.8 + - - -
393A ASP* 1.3 74.4 + - - +
395A THR* 1.4 60.3 + - - +
396A ALA 3.4 2.5 - - - -
397A ALA* 3.2 5.5 + - + +
398A GLN* 2.7 59.2 + - + +
408A VAL* 5.5 7.6 - - + -
412A SER* 6.1 0.2 - - - +
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Residues in contact with THR 395 (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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393A ASP* 2.7 32.8 + - - +
394A ASN* 1.4 80.1 + - - +
396A ALA* 1.3 60.7 + - - +
398A GLN* 3.2 16.2 + - - +
399A LYS* 3.1 39.6 + - - +
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Residues in contact with ALA 396 (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 GLN* 3.2 31.1 - - - +
377A ASN* 3.5 31.2 - - + +
378A ILE* 3.8 11.9 - - + +
393A ASP* 4.7 2.6 + - - +
394A ASN* 3.4 0.6 - - - +
395A THR* 1.3 81.8 + - - +
397A ALA* 1.3 57.7 + - - +
399A LYS* 3.7 1.7 + - - -
400A LEU* 2.9 27.5 + - - +
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ILE* 4.1 11.8 - - + +
391A MET* 3.7 37.4 - - + -
393A ASP 5.5 0.2 + - - -
394A ASN* 3.2 8.4 + - + +
396A ALA* 1.3 75.7 - - - +
398A GLN* 1.3 63.8 + - - +
400A LEU* 3.8 7.0 - - - -
401A CYS* 3.1 32.7 + - - -
408A VAL* 4.3 5.7 - - + +
411A PHE* 4.3 11.7 - - + -
412A SER* 4.9 3.6 - - - +
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Residues in contact with GLN 398 (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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394A ASN* 2.7 40.7 + - - +
395A THR* 3.2 16.2 + - - +
397A ALA* 1.3 78.7 - - - +
399A LYS* 1.3 61.3 + - + +
401A CYS* 3.3 2.6 + - - +
402A ARG* 3.2 36.4 + - - +
408A VAL* 4.2 26.6 - - + +
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Residues in contact with LYS 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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320A LEU* 4.0 38.7 + - + +
322A GLU* 3.0 38.3 + - - +
374A GLN* 3.8 17.0 - - + +
395A THR* 3.1 20.7 + - - +
396A ALA* 3.7 8.3 - - - +
398A GLN* 1.3 72.8 - - + +
400A LEU* 1.3 65.9 + - - +
402A ARG* 3.3 12.1 + - - +
403A LEU* 3.1 30.2 + - + +
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Residues in contact with LEU 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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371A ALA* 3.2 30.7 - - - +
374A GLN* 3.7 9.1 - - + +
375A PHE* 3.5 50.9 - - + +
378A ILE* 3.7 17.9 - - + -
396A ALA 2.9 19.3 + - - +
397A ALA* 4.0 4.7 - - - +
398A GLN 3.4 0.2 - - - -
399A LYS* 1.3 75.3 - - - +
401A CYS* 1.3 57.6 + - - +
403A LEU* 3.5 4.4 + - - +
404A LEU* 3.0 40.1 + - + +
406A LEU* 6.0 0.2 - - + -
411A PHE* 3.7 18.8 - - + -
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Residues in contact with CYS 401 (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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397A ALA 3.1 25.6 + - - +
398A GLN 3.8 3.4 - - - +
399A LYS 3.3 0.2 - - - -
400A LEU* 1.3 75.0 - - - +
402A ARG* 1.3 59.7 + - - +
404A LEU* 4.4 1.6 - - - +
405A GLY* 2.9 24.9 + - - -
406A LEU* 3.0 36.4 + - - +
407A GLY 4.1 1.3 - - - -
408A VAL* 3.7 24.9 - - + -
411A PHE* 3.6 40.6 - - - -
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Residues in contact with ARG 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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320A LEU* 3.6 39.0 - - + +
367A ARG* 5.3 2.1 - - - -
398A GLN* 3.2 22.5 + - - +
399A LYS* 3.5 20.3 - - - +
401A CYS* 1.3 77.2 - - - +
403A LEU* 1.4 62.0 + - + +
404A LEU 3.4 0.7 + - - -
405A GLY* 3.5 8.2 + - - -
631A ASP* 6.0 0.2 - - - +
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Residues in contact with LEU 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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318A ASP 5.2 2.0 - - - +
319A LEU* 3.6 28.7 - - - +
320A LEU* 5.0 9.6 - - + -
367A ARG* 3.7 38.9 + - + +
368A MET* 5.5 1.9 - - - +
370A SER* 3.8 21.3 - - - +
371A ALA* 3.9 29.3 - - + +
374A GLN* 4.1 11.4 - - + +
399A LYS* 3.1 29.9 + - + +
400A LEU* 3.9 4.7 - - - +
402A ARG* 1.4 77.6 - - + +
404A LEU* 1.4 61.3 + - - +
631A ASP* 3.7 16.1 - - - +
634A THR* 4.2 1.9 + - - -
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Residues in contact with LEU 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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368A MET* 3.8 24.0 - - - -
371A ALA* 3.7 22.4 - - + -
375A PHE* 3.5 34.5 - - + -
400A LEU* 3.0 30.4 + - + +
402A ARG 3.3 0.4 - - - -
403A LEU* 1.4 77.3 - - - +
405A GLY* 1.3 54.9 + - - +
406A LEU* 3.5 22.8 - - + +
411A PHE* 6.1 0.4 - - + -
447A THR* 4.6 8.1 - - + -
626A LEU* 3.9 15.0 - - + -
629A SER* 2.6 24.7 + - - -
631A ASP* 4.4 1.3 - - - -
634A THR* 3.6 20.2 - - + +
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Residues in contact with GLY 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 CYS 2.9 8.4 + - - -
402A ARG* 3.5 9.1 + - - -
403A LEU 3.5 0.6 - - - -
404A LEU* 1.3 76.9 - - - +
406A LEU* 1.4 54.7 + - - -
629A SER* 3.1 9.7 + - - -
630A THR* 2.9 49.1 + - - +
631A ASP* 4.1 7.4 - - - +
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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