Contacts of the helix formed by residues 418 - 436 (chain B) in PDB entry 3U44
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 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ASN 3.8 6.7 - - - +
417B GLU* 1.3 84.0 - - + +
419B LYS* 1.3 66.5 + - - +
420B ALA* 3.3 6.7 + - + +
421B LYS* 3.5 19.7 + - + +
422B VAL* 3.1 19.1 + - - +
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A GLN* 5.9 0.4 + - - +
703A ALA* 5.7 2.6 - - - +
410B GLU* 5.3 5.8 - - - +
413B PHE* 4.7 13.5 - - + -
417B GLU 3.3 5.1 + - - -
418B PRO* 1.3 71.2 - - - +
420B ALA* 1.3 80.4 + - + +
422B VAL* 2.8 22.7 + - - +
423B ARG* 2.9 53.9 + - - +
524B ARG* 5.0 25.6 - - - +
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A TYR* 5.1 10.8 - - - +
699A GLN* 6.1 1.8 - - - -
418B PRO* 3.3 5.5 - - + -
419B LYS* 1.3 87.3 - - + +
421B LYS* 1.3 75.4 + - + +
423B ARG* 3.6 14.5 + - - +
424B GLU* 3.3 23.1 + - - +
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A LYS* 5.5 7.7 - - - +
418B PRO* 3.5 20.6 + - + +
419B LYS 3.2 0.4 - - - -
420B ALA* 1.3 80.5 - - + +
422B VAL* 1.3 67.6 + - + +
424B GLU* 2.8 36.3 + - - +
425B GLN* 2.9 25.7 + - + +
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PHE* 3.5 40.8 - - + -
414B PRO* 4.0 10.1 - - + +
417B GLU* 4.2 23.8 - - + +
418B PRO 3.1 22.0 - - - +
419B LYS* 2.8 11.2 + - - +
421B LYS* 1.3 72.9 - - + +
423B ARG* 1.3 55.7 + - - +
425B GLN* 3.2 13.6 + - - +
426B VAL* 2.8 33.6 + - - +
480B TRP* 3.8 20.0 - - + -
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A GLN* 2.7 39.6 + - - +
702A ARG* 3.7 40.1 - - - +
703A ALA* 4.3 18.7 - - - +
410B GLU* 4.0 21.4 + - - +
413B PHE* 4.1 17.9 - - + -
419B LYS* 2.9 58.8 + - - +
420B ALA* 3.6 11.6 - - - +
422B VAL* 1.3 76.2 - - - +
424B GLU* 1.3 53.7 + - + +
426B VAL* 2.9 9.8 + - - +
427B ASP* 2.7 40.0 + - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A TYR* 3.5 31.0 + - + +
671A TYR* 3.9 19.7 + - + +
675A LYS* 3.8 26.5 - - - +
695A TYR* 5.1 2.4 + - - -
699A GLN* 5.8 0.2 + - - -
702A ARG* 6.1 0.7 - - - +
420B ALA* 3.3 21.3 - - - +
421B LYS* 2.8 30.9 + - - +
423B ARG* 1.3 72.2 - - + +
425B GLN* 1.3 57.5 + - + +
427B ASP* 3.1 8.8 + - - +
428B GLN* 2.8 36.3 + - - +
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Residues in contact with GLN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLU* 5.5 3.3 - - - +
421B LYS* 2.9 24.2 + - + +
422B VAL* 3.5 14.9 - - + +
424B GLU* 1.3 77.2 - - + +
426B VAL* 1.3 56.9 + - - +
428B GLN* 3.4 2.8 + - - +
429B LEU* 2.9 29.8 + - - +
473B MET* 3.6 51.2 - - + +
474B LEU* 5.9 0.9 - - - +
476B ASP* 5.6 4.5 + - - +
477B THR* 3.7 22.2 + - + +
480B TRP* 4.7 9.6 + - + -
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 3.3 22.7 - - + -
407B VAL* 3.7 34.8 - - + +
408B LYS* 4.5 14.8 - - + -
413B PHE* 3.9 11.7 - - + -
422B VAL 2.8 22.8 + - - +
423B ARG* 3.1 9.4 - - - +
425B GLN* 1.3 72.9 - - - +
427B ASP* 1.3 63.2 + - - +
429B LEU* 3.2 1.8 + - - +
430B GLU* 2.8 23.7 + - - +
477B THR* 4.4 8.1 - - + -
480B TRP* 3.8 20.4 - - + -
481B ILE* 5.8 0.2 - - + -
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ASP 4.6 0.7 - - - -
635A ASN* 3.3 30.9 + - - +
636A PRO* 2.9 21.0 - - - +
637A TYR* 3.8 8.7 - - + -
671A TYR* 5.8 0.2 - - - -
702A ARG* 2.8 30.6 + - - -
408B LYS* 4.5 9.0 - - - +
423B ARG* 2.7 24.2 + - - +
424B GLU* 3.4 9.4 - - - +
426B VAL* 1.3 80.0 - - - +
428B GLN* 1.3 56.9 + - - +
430B GLU* 2.9 23.0 + - - +
431B ASN* 2.9 13.8 + - - +
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A TYR* 3.3 43.8 + - + -
669A PRO* 5.0 5.1 - - - +
672A GLU* 5.0 7.9 + - - -
424B GLU* 2.8 24.2 + - - +
425B GLN* 3.7 4.3 - - - +
427B ASP* 1.3 71.2 - - - +
429B LEU* 1.3 62.4 + - - +
431B ASN* 3.4 11.1 + - - +
432B TYR* 3.1 21.5 + - - +
470B MET* 4.3 30.7 - - + +
473B MET* 2.9 32.7 - - - +
474B LEU* 5.2 7.6 - - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 3.5 15.3 - - + -
425B GLN 2.9 14.7 + - - +
426B VAL 3.4 8.3 - - - +
427B ASP 3.2 0.2 - - - -
428B GLN* 1.3 75.6 - - - +
430B GLU* 1.3 61.6 - - - +
432B TYR* 3.3 12.8 - - + +
433B CYS* 3.0 39.0 + - - -
438B ILE* 6.0 0.4 - - + -
443B TRP* 4.4 10.5 - - + -
474B LEU* 4.1 36.0 - - + +
477B THR* 3.4 28.9 - - + -
478B ARG* 4.2 9.6 - - + +
481B ILE* 3.5 18.8 - - + -
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ASP* 4.5 0.4 - - - +
635A ASN* 3.0 21.6 + - - +
759A PHE* 3.4 26.5 - - + -
400B TYR* 5.4 2.0 - - + -
404B PHE* 3.3 33.5 - - + +
408B LYS* 2.8 39.5 + - - -
426B VAL 2.8 12.8 + - - +
427B ASP* 2.9 10.6 + - - +
429B LEU* 1.3 75.2 - - - +
431B ASN* 1.3 66.3 + - - +
433B CYS* 3.2 3.8 + - - +
434B ILE* 3.0 37.6 + - + +
816B ARG* 4.8 0.4 - - - -
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Residues in contact with ASN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ASN* 3.1 23.7 + - - -
637A TYR* 3.3 35.2 + - - +
427B ASP 2.9 8.4 + - - -
428B GLN* 3.5 12.0 - - - +
430B GLU* 1.3 74.1 - - - +
432B TYR* 1.3 64.8 + - - +
434B ILE* 3.0 10.4 + - - +
435B ALA* 3.0 24.3 + - - +
816B ARG* 3.6 26.0 + - + +
817B GLN 4.5 1.2 - - - +
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Residues in contact with TYR 432 (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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428B GLN 3.1 10.6 + - - +
429B LEU* 3.3 18.4 - - + +
430B GLU 3.2 0.2 - - - -
431B ASN* 1.3 78.7 - - - +
433B CYS* 1.3 66.6 + - - +
434B ILE 2.9 1.7 + - - -
435B ALA* 3.0 1.7 + - - -
436B TYR* 2.9 70.0 + + - +
438B ILE* 3.3 33.7 - - + -
442B ARG* 5.1 9.0 + - - -
474B LEU* 3.4 33.2 - - + -
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Residues in contact with CYS 433 (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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400B TYR* 3.9 18.2 - - + -
404B PHE* 3.5 15.5 - - + -
429B LEU* 3.0 32.9 + - - +
430B GLU 3.2 4.2 + - - +
432B TYR* 1.3 78.1 - - - +
434B ILE* 1.3 56.2 + - - +
437B GLY* 2.9 24.0 + - - -
438B ILE* 2.9 36.9 + - + +
443B TRP* 3.5 32.3 - - - -
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Residues in contact with ILE 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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759A PHE* 3.9 22.4 - - + -
763A ARG* 4.8 1.1 - - - +
400B TYR* 3.4 34.6 + - + +
430B GLU* 3.0 23.5 + - + +
431B ASN* 3.3 7.6 - - - +
432B TYR 2.9 0.6 + - - -
433B CYS* 1.3 76.7 - - - +
435B ALA* 1.3 65.5 + - - +
436B TYR 3.4 0.2 + - - -
437B GLY* 3.4 8.1 + - - -
816B ARG* 3.0 36.8 - - - +
817B GLN 3.6 6.1 - - - +
818B PHE* 3.5 34.5 - - + -
819B PHE* 3.5 14.7 + - - +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASN 3.0 13.2 + - - +
432B TYR* 3.9 0.9 - - - +
434B ILE* 1.3 77.6 - - - +
436B TYR* 1.3 77.2 + - + +
817B GLN* 3.2 43.2 + - + +
818B PHE 3.5 9.9 - - - +
819B PHE* 3.2 16.3 - - - -
872B GLN* 5.4 0.2 + - - -
873B LYS* 4.2 11.8 - - - +
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Residues in contact with TYR 436 (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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432B TYR* 2.9 58.7 + + + +
435B ALA* 1.3 88.8 - - + +
437B GLY* 1.3 65.3 + - - +
438B ILE* 3.1 17.8 + - + +
819B PHE* 3.5 22.7 - - - -
873B LYS* 3.4 41.2 - - + -
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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