Contacts of the helix formed by residues 434 - 447 (chain B) in PDB entry 5I4V
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 ASP 434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B HIS* 3.8 3.3 + - - -
432B ARG 3.3 3.9 + - - +
433B MET* 1.3 79.4 - - - +
435B LYS* 1.3 58.7 + - - +
436B THR* 2.8 8.9 + - - -
437B GLU* 2.7 36.5 + - - +
438B LEU* 3.1 22.3 + - - +
474B TYR* 2.8 29.4 + - - -
478B LYS* 4.4 2.4 - - - +
479B TYR* 2.7 26.1 + - - +
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.6 18.2 - - + -
308B GLU* 4.0 32.8 - - + +
309B LEU* 4.3 17.7 - - + -
312B GLU 5.2 7.1 + - - -
386B HIS* 3.6 31.3 + - + -
387B ARG* 5.7 4.2 - - - +
434B ASP* 1.3 74.4 + - - +
436B THR* 1.3 66.6 + - - +
438B LEU* 3.3 12.8 + - + +
439B GLY* 3.0 20.4 + - - -
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Residues in contact with THR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 3.5 45.2 - - + +
304B ILE* 4.4 0.7 - - + +
305B LEU* 3.5 34.6 - - - +
434B ASP* 2.8 7.8 + - - -
435B LYS* 1.3 76.9 - - - +
437B GLU* 1.3 62.9 + - - +
439B GLY* 3.2 2.5 + - - -
440B CYS* 3.0 26.2 + - - -
474B TYR* 3.8 30.5 + - + -
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B MET* 3.4 12.9 - - + -
434B ASP* 2.7 49.3 + - - +
436B THR* 1.3 72.7 - - - +
438B LEU* 1.3 61.7 + - - +
440B CYS* 3.5 1.9 + - - +
441B LEU* 3.1 28.1 + - - +
471B LEU* 4.4 10.3 - - + +
474B TYR* 3.9 13.0 - - + -
475B CYS* 4.2 2.1 - - - -
479B TYR* 3.4 9.1 - - - -
485B ARG* 2.6 51.1 + - - +
489B LEU* 3.9 25.6 - - + +
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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
----------------------------------------------------------
308B GLU* 3.3 23.8 - - - +
382B ALA* 3.9 13.2 - - + +
383B SER* 4.7 7.4 - - - -
386B HIS* 3.6 33.4 - - + +
428B MET* 3.7 30.1 - - + -
433B MET* 4.0 8.0 - - - -
434B ASP 3.1 14.0 + - - +
435B LYS* 3.4 15.5 - - - +
436B THR 3.3 0.2 - - - -
437B GLU* 1.3 77.4 - - - +
439B GLY* 1.3 57.2 + - - +
441B LEU* 3.2 8.6 + - + +
442B ARG* 2.9 45.8 + - + +
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Residues in contact with GLY 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 3.4 22.1 - - - +
308B GLU* 3.7 27.1 - - - +
353B TRP* 4.1 2.9 - - - -
435B LYS 3.0 11.3 + - - -
436B THR 3.2 1.1 + - - -
438B LEU* 1.3 75.5 - - - +
440B CYS* 1.3 58.0 + - - +
442B ARG* 3.2 2.9 + - - +
443B ALA* 2.8 29.5 + - - +
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Residues in contact with CYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 3.9 28.5 - - - -
304B ILE* 4.0 17.9 - - - -
436B THR* 3.0 22.6 + - - +
437B GLU 3.8 4.5 - - - +
439B GLY* 1.3 73.6 - - - +
441B LEU* 1.3 66.0 + - - +
443B ALA* 3.1 3.3 + - - -
444B ILE* 2.9 22.4 + - - +
467B VAL* 3.4 21.9 - - + +
470B SER* 5.6 0.4 - - - -
471B LEU* 3.8 33.7 - - + -
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ALA* 6.5 0.7 - - + -
428B MET* 5.9 1.1 - - + -
433B MET* 4.0 30.3 - - + -
437B GLU 3.1 17.4 + - - +
438B LEU* 3.5 10.1 - - + +
440B CYS* 1.3 76.2 - - - +
442B ARG* 1.3 64.1 + - + +
444B ILE* 3.2 7.4 + - + +
445B ILE* 3.0 30.1 + - + +
471B LEU* 4.2 13.2 - - + -
489B LEU* 3.9 38.6 - - + +
490B LEU* 4.2 10.1 - - + -
492B ARG* 5.1 2.9 - - + -
493B LEU* 3.8 30.2 - - + +
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Residues in contact with ARG 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 2.5 39.7 + - - -
311B VAL* 5.5 3.2 - - - +
350B LEU* 3.4 29.1 - - - +
353B TRP* 3.3 42.2 - - + +
379B LEU* 3.2 43.9 + - + +
380B LEU* 5.0 2.6 - - - +
382B ALA* 4.2 18.2 - - + -
383B SER* 3.9 18.1 + - - +
438B LEU* 2.9 38.5 + - + +
439B GLY 3.6 1.6 - - - +
440B CYS 3.2 0.4 - - - -
441B LEU* 1.3 77.2 - - + +
443B ALA* 1.3 57.7 - - - +
445B ILE* 3.3 4.3 + - + -
446B LEU* 2.8 25.8 + - - +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 4.6 6.1 - - + -
353B TRP* 3.9 4.6 - - - -
357B ILE* 4.4 24.2 - - + -
439B GLY 2.8 16.8 + - - +
440B CYS* 3.1 7.4 + - - +
442B ARG* 1.3 74.9 - - - +
444B ILE* 1.3 58.9 + - - +
446B LEU* 3.4 7.5 - - - +
447B PHE* 2.9 39.0 + - + -
467B VAL* 4.0 20.0 - - + -
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 4.1 3.8 - - + -
440B CYS 2.9 18.0 + - - +
441B LEU* 3.4 12.8 - - + +
443B ALA* 1.3 74.4 - - - +
445B ILE* 1.3 61.3 + - - +
447B PHE 3.5 1.0 + - - -
464B ARG* 2.6 59.2 + - - +
467B VAL* 3.5 24.2 - - + -
468B TYR* 3.9 27.4 - - + +
471B LEU* 4.1 13.9 - - + -
490B LEU* 3.9 19.7 - - + -
493B LEU* 3.7 23.1 - - + -
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLY* 4.4 10.1 - - - +
378B GLU* 3.9 38.6 - - + +
379B LEU* 4.0 15.9 - - + -
382B ALA* 4.9 5.6 - - + -
441B LEU* 3.0 23.2 + - + +
442B ARG* 3.3 12.8 + - + +
444B ILE* 1.3 78.1 - - - +
446B LEU* 1.3 67.6 + - - +
448B ASN* 3.5 17.0 + - - +
464B ARG* 4.7 4.9 - - - +
493B LEU* 4.6 18.4 - - + -
496B LEU* 3.4 32.8 - - + -
497B ARG* 5.9 3.7 + - - +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TRP* 3.8 24.5 - - + -
354B ALA* 4.4 4.9 - - + -
357B ILE* 4.2 22.9 - - + -
360B PHE* 4.1 36.6 - - + -
371B LEU* 3.6 30.1 - - + +
372B LEU* 4.4 14.1 - - + -
375B GLY* 5.7 1.1 - - - -
379B LEU* 4.3 19.7 - - + -
442B ARG 2.8 17.3 + - - +
443B ALA* 3.4 4.5 - - - +
445B ILE* 1.3 80.3 - - - +
447B PHE* 1.3 65.5 + - + +
448B ASN* 2.8 9.5 + - - +
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Residues in contact with PHE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 4.2 15.0 - - + -
357B ILE* 3.7 33.2 - - + -
358B PRO 3.7 13.2 - - - -
360B PHE* 4.2 26.0 - + + -
363B LEU* 4.5 2.5 - - + -
371B LEU* 4.4 13.5 - - + -
443B ALA* 2.9 30.6 + - + +
444B ILE 4.4 0.2 - - - +
445B ILE 3.3 0.8 - - - -
446B LEU* 1.3 72.9 - - + +
448B ASN* 1.3 53.1 - - - +
449B PRO* 3.3 6.6 - - - +
460B VAL* 3.6 22.6 - - + +
463B LEU* 3.7 34.8 - - + -
464B ARG* 2.2 38.1 + - + +
467B VAL* 4.2 13.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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