Contacts of the helix formed by residues 526 - 534 (chain B) in PDB entry 1ULT
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 LEU 526 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ILE* 5.2 0.6 - - - +
518B PRO* 2.6 37.6 + - + +
519B ARG* 3.3 22.0 - - - +
520B THR* 4.4 8.1 - - - +
525B PHE* 1.3 67.3 - - - +
527B LYS* 1.3 56.0 + - - +
528B ARG* 3.0 52.6 + - + +
529B ALA* 3.1 21.5 + - + +
530B LEU* 3.7 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ASP* 4.3 4.0 + - - -
436B ASP* 3.2 24.1 + - + +
447B SER* 3.1 16.6 + - - -
448B VAL* 4.7 3.0 - - - +
451B GLU* 2.7 34.0 + - - -
464B ALA* 4.7 0.7 - - - -
465B VAL 3.0 19.3 + - - +
466B VAL* 3.6 22.4 - - + -
525B PHE* 2.7 36.8 + - + +
526B LEU* 1.3 68.7 - - - +
528B ARG* 1.3 64.8 + - - +
529B ALA 3.3 0.2 - - - -
530B LEU* 3.7 13.8 - - + +
531B ARG* 2.9 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY* 3.4 24.7 + - - -
188B THR* 3.9 34.7 + - + +
526B LEU* 3.0 22.6 + - + +
527B LYS* 1.3 78.9 - - - +
529B ALA* 1.3 63.0 + - - +
531B ARG* 3.1 23.7 + - - +
532B GLU* 3.5 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B PRO* 4.8 10.8 - - + -
526B LEU* 3.1 23.0 + - + +
528B ARG* 1.3 79.0 - - - +
530B LEU* 1.3 59.8 + - - +
532B GLU* 3.1 10.1 + - - +
533B GLN* 2.9 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ALA* 4.0 19.1 - - + -
466B VAL* 4.2 20.8 - - + +
468B ILE* 4.4 1.6 - - - +
480B VAL* 3.9 30.3 - - + -
517B ILE* 3.9 22.4 - - + -
518B PRO* 4.6 14.1 - - + -
525B PHE* 5.7 0.2 - - + -
526B LEU 3.7 7.2 + - - +
527B LYS* 3.3 20.7 + - + +
529B ALA* 1.3 77.7 - - + +
531B ARG* 1.3 62.0 + - - +
533B GLN* 4.3 14.8 - - - +
534B TYR* 3.2 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LYS* 4.4 8.0 + - - +
436B ASP* 2.8 55.3 + - - +
466B VAL* 4.5 13.0 - - + +
467B ALA* 4.3 22.4 + - - +
468B ILE* 4.1 12.1 - - - +
469B PRO* 5.1 2.9 - - - +
527B LYS* 2.9 58.0 + - - +
528B ARG* 3.1 17.1 - - - +
529B ALA 3.3 0.2 - - - -
530B LEU* 1.3 75.4 - - - +
532B GLU* 1.3 58.2 + - - +
534B TYR 3.9 1.0 - - - -
535B LYS* 3.3 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B ARG 3.5 8.9 + - - +
529B ALA* 3.1 10.9 + - - +
531B ARG* 1.3 79.8 - - - +
533B GLN* 1.3 66.8 + - + +
535B LYS* 3.0 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B PRO* 4.6 10.7 - - - +
529B ALA* 2.9 38.1 + - + +
530B LEU* 3.3 11.1 + - - +
532B GLU* 1.3 77.9 - - - +
534B TYR* 1.3 88.5 + - + +
535B LYS* 3.3 2.6 + - - +
536B ASN 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 3.2 23.9 - - + +
478B LEU* 3.4 32.5 - - + -
480B VAL* 4.3 13.7 - - + +
512B VAL* 3.4 42.2 - - + +
513B PHE 4.9 1.9 + - - -
514B ALA* 5.5 2.1 - - - +
530B LEU* 3.2 32.8 + - + +
531B ARG 3.9 0.2 - - - -
533B GLN* 1.3 99.1 + - + +
535B LYS* 1.3 63.8 + - - +
536B ASN 3.2 3.8 + - - -
537B TYR* 3.2 31.7 + + + +
----------------------------------------------------------
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