Contacts of the helix formed by residues 391 - 403 (chain A) in PDB entry 4I6J
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 SER 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A MET* 5.7 0.5 - - - +
338A TRP* 3.3 29.0 - - - +
339A ASP 4.3 0.8 + - - -
383A LEU* 4.6 2.1 - - - +
384A THR* 4.5 0.7 - - - +
390A VAL* 1.3 81.9 - - - +
392A TRP* 1.3 65.6 + - - +
393A GLU* 3.1 28.9 + - - +
394A SER* 3.2 18.3 + - - -
395A GLY 3.7 3.5 + - - -
90B TYR* 3.4 37.6 + - - -
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Residues in contact with TRP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE 3.9 1.1 - - - -
325A ASP* 3.7 24.0 - - - -
326A ARG 3.4 37.5 - - - -
327A MET* 3.7 7.9 - - - +
333A CYS* 3.6 15.0 - - - -
338A TRP* 3.5 20.2 - + - +
384A THR* 3.7 17.0 - - + +
390A VAL 3.6 1.2 + - - -
391A SER* 1.3 70.1 + - - +
393A GLU* 1.3 67.6 + - + +
394A SER 3.0 2.2 - - - -
395A GLY* 3.2 2.8 + - - +
396A VAL* 2.9 48.0 + - + +
412A ALA* 4.2 5.2 - - + -
415A TRP* 3.9 24.4 - - + +
416A MET* 3.5 34.3 - - + -
419A SER* 3.6 16.4 - - - +
421A SER* 3.4 23.9 + - - -
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASP 3.9 16.6 - - - +
326A ARG* 3.1 27.2 + - - +
327A MET* 2.6 38.9 + - - +
328A GLU 4.4 1.0 + - - -
391A SER* 3.1 14.2 + - - +
392A TRP* 1.3 93.8 - - + +
394A SER* 1.3 58.8 + - - +
396A VAL* 3.4 8.5 + - - +
397A ARG* 3.1 26.0 + - - +
90B TYR* 3.8 22.6 - - + -
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.9 21.3 - - - +
383A LEU* 4.7 1.1 - - - -
390A VAL* 4.0 9.7 - - - +
391A SER 3.2 10.6 + - - -
392A TRP 3.0 0.8 - - - -
393A GLU* 1.3 77.9 - - - +
395A GLY* 1.3 63.7 + - - +
397A ARG* 3.2 29.9 + - - +
398A VAL* 3.2 28.4 + - - +
90B TYR* 3.4 21.5 + - - -
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Residues in contact with GLY 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP* 4.2 5.2 - - - -
383A LEU* 3.7 12.0 - - - +
391A SER 3.7 5.3 + - - -
392A TRP 3.2 4.7 + - - -
394A SER* 1.3 74.5 - - - +
396A VAL* 1.3 65.1 + - - +
398A VAL* 3.4 0.7 + - - +
399A PHE* 3.0 26.0 + - - +
415A TRP* 3.5 35.5 - - - -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASP* 4.8 19.5 - - + +
392A TRP* 2.9 31.8 + - + +
393A GLU* 3.4 10.3 - - - +
395A GLY* 1.3 76.0 - - - +
397A ARG* 1.3 58.6 + - - +
399A PHE 3.2 0.3 + - - -
400A ASP* 2.8 30.6 + - + +
408A PHE 6.1 0.2 - - - +
411A ASN* 3.2 21.5 - - + +
412A ALA* 4.0 15.5 - - - +
415A TRP* 3.7 28.4 - - + +
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.3 11.7 - - - +
393A GLU 3.1 9.6 + - - +
394A SER* 3.2 38.8 + - - +
396A VAL* 1.3 79.9 - - - +
398A VAL* 1.3 64.4 + - + +
400A ASP* 3.2 9.8 + - + +
401A GLU* 3.2 37.6 + - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.4 14.6 - - + -
348A TRP* 3.7 36.1 - - + -
349A ALA* 4.6 14.1 - - + -
362A MET* 4.3 9.4 - - + -
366A ARG* 4.9 1.3 - - - +
394A SER 3.2 12.9 + - - +
395A GLY 3.8 2.5 - - - +
397A ARG* 1.3 75.5 - - + +
399A PHE* 1.3 65.4 + - + +
401A GLU* 3.1 20.5 + - - +
402A LEU* 3.1 35.0 + - + +
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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
----------------------------------------------------------
348A TRP* 3.7 23.6 - + - -
365A LEU* 3.6 25.8 - - + -
371A ILE* 4.4 11.7 - - + -
376A ARG* 4.4 25.6 - - + -
379A VAL* 3.7 20.0 - - + -
380A ALA* 5.5 0.4 - - + -
395A GLY 3.0 16.7 + - - +
396A VAL 3.7 0.7 - - - +
398A VAL* 1.3 74.5 - - + +
400A ASP* 1.3 62.5 + - - +
402A LEU* 4.4 1.1 - - - +
403A LEU* 2.8 54.8 + - + +
406A ALA* 3.9 2.3 - - - +
411A ASN* 3.6 20.9 - - - +
415A TRP* 3.3 32.3 - + - -
428B TRP* 5.8 1.8 - - - -
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.5 19.9 - - - +
69A ARG* 2.7 55.8 + - - +
396A VAL* 2.8 24.1 + - + +
397A ARG* 3.5 11.6 - - + +
398A VAL 3.2 0.4 - - - -
399A PHE* 1.3 73.7 - - - +
401A GLU* 1.3 56.2 + - + +
406A ALA* 3.8 7.8 - - - +
407A ASP* 5.3 3.6 - - - -
408A PHE* 5.5 0.7 + - - -
411A ASN* 4.1 6.1 + - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 3.3 37.5 + - - +
64A SER* 3.7 18.1 - - - +
65A VAL* 4.4 0.7 - - - +
66A GLY* 3.1 25.1 + - - +
68A ASN* 6.1 0.3 - - - +
69A ARG* 3.7 8.8 + - - +
366A ARG* 5.9 1.2 + - - -
397A ARG* 3.2 26.1 + - + +
398A VAL* 3.1 13.8 + - - +
399A PHE 3.1 0.4 - - - -
400A ASP* 1.3 81.3 - - - +
402A LEU* 1.3 71.6 + - + +
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Residues in contact with LEU 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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66A GLY* 5.1 7.2 - - - -
67A ILE* 6.1 3.8 - - + -
68A ASN* 4.8 8.3 + - - +
69A ARG* 4.7 3.6 - - - -
349A ALA 5.1 1.3 - - - +
362A MET* 5.2 1.6 - - + +
365A LEU* 3.7 34.3 - - + +
366A ARG* 3.6 61.7 - - + +
369A GLY* 3.4 23.0 - - - -
398A VAL* 3.1 28.2 + - + +
401A GLU* 1.3 94.9 - - + +
403A LEU* 1.3 60.1 + - - +
404A LEU* 3.6 2.1 + - - +
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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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69A ARG* 3.4 15.0 + - - -
365A LEU* 4.2 13.2 - - + -
369A GLY 3.3 16.8 - - - +
370A TRP* 4.0 9.9 - - - -
371A ILE* 4.5 3.8 - - + +
376A ARG* 3.4 33.0 - - + +
399A PHE* 2.8 46.3 + - + +
401A GLU 3.9 0.6 - - - -
402A LEU* 1.3 69.6 - - - +
404A LEU* 1.3 68.8 + - + +
405A ASP* 3.0 31.8 + - - +
406A ALA* 3.2 22.6 + - + +
411A ASN* 5.1 1.6 - - - +
428B TRP* 5.2 0.9 - - - +
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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