Contacts of the helix formed by residues 433 - 446 (chain B) in PDB entry 4I5L
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 PRO 433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B CYS* 6.0 0.4 - - - -
430B GLU* 5.7 3.4 - - - +
431B ALA 3.4 7.2 - - - +
432B LEU* 1.3 92.9 - - + +
434B PHE* 1.3 67.2 + - - +
435B GLN* 4.5 5.6 - - + +
436B ASP* 3.0 37.8 + - - +
437B CYS* 3.0 9.9 + - - +
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Residues in contact with PHE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B MET* 3.8 31.6 - - + -
413B LEU* 3.9 16.4 - - + -
414B GLU* 3.6 54.5 - - + +
417B TYR* 3.6 35.2 - + + -
421B CYS* 5.7 0.4 - - - -
432B LEU 3.5 1.8 + - - -
433B PRO* 1.3 72.3 - - - +
435B GLN* 1.3 75.5 + - - +
437B CYS* 3.4 2.6 + - + +
438B LEU* 2.7 49.8 + - + +
471B PHE* 4.4 6.5 - + - -
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Residues in contact with GLN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 4.6 16.4 - - - +
433B PRO* 3.0 5.1 + - + +
434B PHE* 1.3 102.8 - - - +
436B ASP* 1.3 67.4 + - - +
438B LEU* 3.9 9.4 - - + +
439B CYS* 3.1 28.6 + - - +
295C ARG* 4.9 10.1 - - - +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU* 4.0 21.5 - - + +
433B PRO* 3.0 29.5 + - + +
435B GLN* 1.3 78.8 - - - +
437B CYS* 1.3 66.2 + - - +
439B CYS* 3.4 6.3 + - - +
440B GLN* 3.0 24.3 + - - +
264C ASN* 4.6 12.3 + - - +
267C TYR* 3.9 18.4 - - + +
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Residues in contact with CYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B TYR* 3.6 46.0 - - + +
432B LEU* 3.8 14.4 - - + +
433B PRO 3.0 7.3 + - - +
434B PHE* 3.5 8.3 - - + +
436B ASP* 1.3 77.5 - - - +
438B LEU* 1.3 63.4 + - - +
440B GLN* 3.3 5.5 + - - +
441B MET* 2.9 36.2 + - - +
470B THR* 3.8 21.8 - - - -
471B PHE* 4.3 8.1 - - - -
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 4.1 29.6 - - + -
413B LEU* 3.8 28.9 - - + -
434B PHE* 2.7 37.0 + - + +
435B GLN* 3.9 11.7 - - + +
436B ASP 3.4 0.2 - - - -
437B CYS* 1.3 74.4 - - - +
439B CYS* 1.3 57.8 + - - +
441B MET* 3.1 8.6 + - + -
442B LEU* 2.9 54.8 + - + +
453B ILE* 5.2 0.7 - - + -
471B PHE* 5.7 1.6 - - + -
295C ARG* 4.9 11.4 - - - +
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Residues in contact with CYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B GLN 3.1 18.6 + - - +
436B ASP* 3.6 6.5 - - - +
438B LEU* 1.3 76.2 - - - +
440B GLN* 1.3 62.8 + - - +
442B LEU* 3.2 13.2 + - - +
443B ASP* 3.0 22.2 + - - -
264C ASN* 6.3 0.9 - - - -
267C TYR* 4.3 10.5 - - - -
291C PRO* 6.2 2.0 - - - -
292C ALA 5.5 0.7 - - - -
294C ARG* 3.6 42.7 - - + -
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Residues in contact with GLN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B LEU* 3.5 23.6 - - - +
436B ASP 3.0 12.7 + - - +
437B CYS* 3.5 9.1 - - - +
439B CYS* 1.3 76.4 - - - +
441B MET* 1.3 72.6 + - + +
443B ASP* 3.2 4.3 + - - +
444B LEU* 2.8 26.3 + - - +
466B VAL* 5.7 2.4 - - - +
477B TYR* 6.3 1.6 - - - -
91C TYR* 2.8 27.2 + - - +
266C CYS 5.2 0.8 - - - +
267C TYR* 3.5 42.5 - - + +
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Residues in contact with MET 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B CYS* 2.9 24.1 + - - +
438B LEU* 3.1 10.5 + - + +
440B GLN* 1.3 106.2 - - + +
442B LEU* 1.3 59.4 + - - +
444B LEU* 3.5 17.9 - - + +
445B VAL* 2.8 35.8 + - - +
453B ILE* 5.4 2.2 - - + -
466B VAL* 5.1 1.8 - - + -
467B PHE* 3.8 43.7 - - + -
470B THR* 4.0 25.6 - - + +
471B PHE* 3.8 22.7 - - + -
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B LEU* 2.9 40.2 + - + +
439B CYS* 3.2 8.7 + - - +
441B MET* 1.3 72.2 - - - +
443B ASP* 1.3 61.3 + - - +
445B VAL* 4.5 0.7 - - - +
446B LYS* 2.9 28.6 + - - -
447B PRO* 3.7 27.6 - - + +
451B GLY* 5.9 1.1 - - - +
452B LYS 6.2 0.7 - - - +
453B ILE* 4.3 19.3 - - + -
294C ARG* 4.8 13.2 - - + +
295C ARG 3.8 25.4 - - - +
296C GLY* 4.0 21.8 - - - -
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Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B CYS 3.0 12.3 + - - -
440B GLN 3.2 6.7 + - - +
442B LEU* 1.3 76.0 - - - +
444B LEU* 1.3 65.8 + - - +
446B LYS* 3.8 1.6 + - - +
63C HIS* 3.4 19.0 + - - -
91C TYR* 3.9 6.6 - - + +
92C TYR* 2.5 37.6 + - + -
267C TYR* 2.5 33.3 + - - +
294C ARG* 2.5 47.1 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B GLN 2.8 17.2 + - - +
441B MET* 3.5 15.7 - - + +
443B ASP* 1.3 77.9 - - - +
445B VAL* 1.3 75.7 + - + +
446B LYS* 4.9 0.7 - - - +
461B CYS* 3.8 14.8 - - - +
463B LEU* 3.6 38.3 - - + +
466B VAL* 3.8 28.5 - - + -
467B PHE* 3.9 12.3 - - + +
91C TYR* 3.5 42.3 - - + +
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B MET 2.8 24.2 + - - +
442B LEU* 5.0 0.2 - - - -
444B LEU* 1.3 82.9 - - + +
446B LYS* 1.3 74.9 + - - +
447B PRO* 3.6 27.5 - - + +
453B ILE* 4.2 20.0 - - + -
457B ASP* 4.3 10.0 - - + +
458B LEU* 3.8 16.6 - - + -
461B CYS* 3.5 22.6 - - + +
467B PHE* 3.5 30.5 - - + -
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Residues in contact with LYS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B LEU 2.9 15.7 + - - -
443B ASP 4.1 0.7 - - - +
444B LEU 3.6 0.9 - - - +
445B VAL* 1.3 80.1 - - - +
447B PRO* 1.4 74.9 - - - +
448B ARG* 3.8 0.7 + - - -
457B ASP* 4.6 2.4 - - - +
19C GLU 5.0 3.1 - - - -
20C CYS* 3.1 38.6 + - - -
21C LYS* 4.9 8.1 - - - +
63C HIS* 5.8 3.6 - - + +
92C TYR* 3.5 31.5 - - + +
95C GLU* 5.3 2.0 + - - -
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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