Contacts of the helix formed by residues 554 - 564 (chain B) in PDB entry 4N41
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 PHE 554 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 3.7 35.0 - + + -
485B PHE* 3.8 29.2 - + - -
519B VAL* 3.8 22.0 - - + -
543B LEU* 5.3 3.6 - - + -
545B ARG* 3.7 44.0 - - + -
549B VAL* 4.1 3.8 - - + -
550B PRO 4.5 1.8 - - - -
551B GLN 3.1 14.2 + - - +
552B ASP 2.9 1.2 - - - -
553B GLU* 1.3 85.4 - - + +
555B ALA* 1.3 63.2 + - - +
556B LEU 3.4 2.7 - - - -
557B ALA* 3.4 6.9 + - + +
558B LEU* 3.0 30.4 + - + +
570B LEU* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLN* 4.4 7.4 - - - +
551B GLN 4.2 1.0 + - - -
552B ASP* 3.1 29.9 + - - +
553B GLU 3.5 0.2 - - - -
554B PHE* 1.3 77.8 - - - +
556B LEU* 1.3 58.5 + - - +
558B LEU* 3.3 12.7 + - - +
559B GLU* 2.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLN* 3.5 41.5 + - + +
517B GLU* 4.6 13.0 - - + -
520B TRP* 3.5 38.1 - - + -
554B PHE 3.4 0.2 - - - -
555B ALA* 1.3 78.7 - - - +
557B ALA* 1.3 57.7 + - - +
559B GLU* 3.2 6.3 + - + +
560B ALA* 2.9 28.1 + - + +
563B ARG* 3.9 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 6.0 0.7 - - + -
516B GLN 4.8 0.8 + - - -
519B VAL* 4.0 24.9 - - + -
520B TRP* 3.9 21.5 - - + +
523B LEU* 4.0 20.2 - - + +
543B LEU* 5.8 1.3 - - + -
553B GLU 5.5 0.2 + - - -
554B PHE* 3.4 11.9 + - + +
555B ALA 3.3 0.4 - - - -
556B LEU* 1.3 75.5 - - - +
558B LEU* 1.3 64.9 + - + +
560B ALA* 3.3 2.3 + - - +
561B LEU* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LEU* 3.8 28.7 - - + -
551B GLN* 6.2 1.3 - - - +
554B PHE* 3.0 24.6 + - + +
555B ALA* 3.4 12.3 - - - +
557B ALA* 1.3 79.6 - - + +
559B GLU* 1.3 58.8 + - + +
561B LEU* 3.2 5.9 + - - +
562B ALA* 2.9 27.5 + - - +
568B TYR* 3.4 41.4 - - + +
570B LEU* 4.2 19.3 - - + -
623B ALA* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ALA* 2.9 17.8 + - + +
556B LEU* 3.2 12.5 + - + +
558B LEU* 1.3 76.8 - - + +
560B ALA* 1.3 58.2 + - - +
562B ALA* 3.1 14.7 + - - +
563B ARG* 2.9 54.1 + - - +
568B TYR* 5.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B TRP* 3.4 46.2 - - + -
556B LEU* 2.9 17.9 + - + +
557B ALA 3.7 0.7 - - - +
559B GLU* 1.3 76.8 - - - +
561B LEU* 1.3 60.9 + - - +
563B ARG* 3.6 25.5 + - - +
564B GLU* 3.4 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B TRP* 5.0 1.6 - - + -
523B LEU* 3.6 24.9 - - + -
527B LEU* 4.1 18.2 - - + -
541B VAL* 3.7 18.8 - - + -
543B LEU* 3.7 24.7 - - + -
557B ALA 2.9 17.9 + - - +
558B LEU* 3.5 7.4 - - - +
560B ALA* 1.3 75.0 - - - +
562B ALA* 1.3 62.3 + - - +
564B GLU* 3.2 6.2 + - - +
565B GLY 3.2 2.8 + - - -
566B ILE* 3.0 63.0 + - + +
568B TYR* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 562 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU 2.9 14.1 + - - +
559B GLU* 3.1 22.0 + - - +
561B LEU* 1.3 73.9 - - - +
563B ARG* 1.3 61.1 - - - +
565B GLY* 2.9 21.0 + - - -
566B ILE 4.6 3.8 - - - -
568B TYR* 4.4 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 563 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU* 3.9 24.7 - - - +
559B GLU* 2.9 32.6 + - - +
560B ALA* 3.8 26.3 - - - +
562B ALA* 1.3 75.3 - - - +
564B GLU* 1.3 63.3 + - - +
565B GLY 3.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B TRP* 6.1 1.6 - - - -
531B ARG* 5.6 1.0 + - - -
537B LEU* 3.4 32.1 - - + +
560B ALA 3.4 10.8 + - - +
561B LEU* 3.2 9.3 + - - +
562B ALA 3.1 1.0 - - - -
563B ARG* 1.3 81.3 - - - +
565B GLY* 1.3 60.1 + - - +
566B ILE* 3.1 17.5 + - + +
----------------------------------------------------------
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