Contacts of the helix formed by residues 435 - 446 (chain B) in PDB entry 1ZUM
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 435 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ASP* 3.3 18.3 + - - +
433B THR* 3.1 8.2 + - - +
434B LYS* 1.3 77.5 - - - +
436B LEU* 1.3 65.3 + - - +
437B ASP* 3.2 12.5 + - - +
438B LYS* 2.9 43.8 + - + +
439B ALA* 3.0 23.7 + - - +
434C LYS* 3.4 27.2 - - - +
436C LEU* 4.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ASP* 1.3 71.4 - - - +
437B ASP* 1.3 64.8 + - - +
439B ALA* 3.3 2.4 + - - +
440B ASN* 2.9 50.6 + - - +
433C THR 4.2 4.0 - - - +
434C LYS* 2.8 21.5 + - - +
435C ASP 4.3 0.7 - - - -
436C LEU* 3.7 35.8 - - + +
439C ALA* 4.3 16.4 - - + -
440C ASN* 5.6 2.5 - - - +
453C VAL* 3.6 28.7 - - + -
454C ASN* 3.6 18.8 - - - +
493D VAL* 4.2 12.8 - - + -
494D LYS 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ASP* 3.2 10.0 + - - +
436B LEU* 1.3 87.1 - - - +
438B LYS* 1.3 60.8 + - + +
440B ASN* 3.3 2.1 + - - -
441B TYR* 2.8 33.0 + - - +
434C LYS* 4.7 3.8 + - - +
454C ASN* 4.8 5.7 + - - -
494D LYS* 4.0 19.2 - - - +
495D VAL 5.5 0.6 - - - -
496D PRO* 3.7 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B MET* 4.2 21.5 - - + +
279B SER* 4.9 7.7 + - - -
280B ASP* 3.4 24.0 + - - +
311B GLN* 5.3 1.2 + - - +
413B ILE* 3.9 24.2 - - + -
433B THR* 3.9 15.3 - - + +
435B ASP* 2.9 36.4 + - + +
437B ASP* 1.3 72.9 - - + +
439B ALA* 1.3 58.2 + - - +
441B TYR* 3.7 1.9 - - - +
442B LEU* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B VAL* 5.0 3.9 - - - +
433B THR* 3.8 17.2 - - + +
435B ASP 3.0 18.1 + - - +
436B LEU 3.6 3.8 - - - +
438B LYS* 1.3 76.7 - - - +
440B ASN* 1.3 59.1 + - - +
442B LEU* 4.2 3.0 - - - +
443B SER* 3.0 32.9 + - - -
453B VAL* 4.0 25.3 - - + +
436C LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 4.4 5.5 + - - -
3109A EDO 4.0 13.7 - - - -
436B LEU* 2.9 42.5 + - - +
437B ASP* 4.0 3.3 + - - +
439B ALA* 1.3 73.4 - - - +
441B TYR* 1.3 66.1 + - - +
443B SER* 3.4 9.1 + - - -
444B GLN* 3.2 24.6 + - - +
436C LEU* 5.6 2.3 - - - +
151D PHE* 4.8 6.9 - - - -
493D VAL* 3.8 19.8 - - - +
494D LYS 4.8 1.2 + - - -
495D VAL* 4.0 23.3 - - + +
496D PRO* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 5.8 5.8 - - + +
413B ILE* 3.5 41.1 - - + -
414B GLU* 3.8 27.5 - - + +
417B VAL* 3.9 21.5 - - + +
437B ASP 2.8 22.8 + - - +
438B LYS* 3.7 3.1 - - - +
440B ASN* 1.3 75.9 - - - +
442B LEU* 1.3 58.1 + - + +
444B GLN* 3.8 8.7 + - - +
445B ALA* 3.0 36.9 + - + +
496D PRO* 4.2 25.7 - - + +
497D GLN* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 4.5 13.5 - - + -
278B MET* 4.0 16.8 - - + -
413B ILE* 3.7 30.3 - - + -
416B VAL* 4.3 10.8 - - + -
417B VAL* 3.5 29.4 - - + -
431B VAL* 3.3 41.1 - - + -
438B LYS 2.8 17.0 + - - +
439B ALA 4.2 0.9 - - - +
441B TYR* 1.3 74.9 - - + +
443B SER* 1.3 65.7 + - - +
444B GLN 3.1 1.3 - - - -
445B ALA* 4.4 1.3 - - - +
446B LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.9 3.1 + - - -
489A LYS* 2.8 30.3 + - - +
491A VAL* 4.0 16.8 - - - +
3109A EDO 2.8 28.2 + - - -
431B VAL* 4.9 0.4 - - - +
439B ALA 3.0 20.5 + - - -
440B ASN* 3.4 7.8 + - - -
441B TYR 3.5 0.2 - - - -
442B LEU* 1.3 76.5 - - - +
444B GLN* 1.3 57.1 + - - +
446B LEU 4.2 0.2 - - - +
451B VAL* 3.9 28.9 - - - +
453B VAL* 4.5 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.9 7.8 - - + +
77A ARG* 6.3 0.2 - - - +
155A ARG* 3.5 25.5 + - - +
157A GLU* 4.2 3.1 - - - +
489A LYS* 3.0 19.4 + - - +
3109A EDO 4.3 9.7 - - - -
440B ASN 3.2 18.8 + - - +
441B TYR* 3.8 7.8 + - - +
442B LEU 3.1 0.4 - - - -
443B SER* 1.3 79.4 + - - +
445B ALA* 1.3 62.7 + - - +
446B LEU 3.9 0.3 - - - +
495D VAL* 5.9 1.4 - - - +
497D GLN 2.7 29.3 + - - -
498D LYS* 4.0 5.1 - - - +
499D ASN* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.0 29.6 - - + +
417B VAL* 3.9 29.6 - - + +
421B ASN* 3.0 21.1 + - - -
441B TYR* 3.0 26.7 + - + +
442B LEU 4.1 0.9 - - - +
444B GLN* 1.3 75.7 - - - +
446B LEU* 1.3 63.5 + - - +
447B GLN* 3.3 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LYS* 2.8 28.8 + - - -
274B PRO* 4.9 0.9 - - + -
276B ILE* 3.9 15.3 - - + -
417B VAL* 4.9 5.8 - - - -
420B ALA* 3.8 28.7 - - + -
421B ASN* 3.6 9.0 - - - +
429B ALA* 3.8 27.6 - - + -
430B ALA 4.7 0.4 - - - +
431B VAL* 3.7 28.0 - - + -
442B LEU* 2.9 32.4 + - + +
444B GLN 4.4 0.2 - - - -
445B ALA* 1.3 70.8 - - - +
447B GLN* 1.3 60.6 + - - +
448B ALA 3.1 5.4 + - - -
451B VAL* 4.1 19.0 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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