Contacts of the helix formed by residues 550 - 558 (chain J) in PDB entry 4E2I
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 LYS 550 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396J CYS 3.6 0.6 + - - -
397J LEU 2.8 32.4 + - - +
398J LEU* 4.0 4.8 - - - +
399J PRO* 4.8 2.0 - - - +
430J SER 5.4 0.4 + - - -
548J ARG* 2.7 32.7 + - + +
549J PRO* 1.3 72.6 - - - +
551J ASP* 1.3 64.0 + - - +
552J TYR* 3.0 39.6 + - + +
553J LEU* 3.6 27.5 + - + +
554J LYS* 3.6 15.8 + - - +
11U GLU* 4.1 12.8 - - - +
14U ILE* 3.3 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 551 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549J PRO 4.7 6.1 - - - +
550J LYS* 1.3 69.1 - - - +
552J TYR* 1.3 61.5 + - - +
553J LEU 3.0 4.7 - - - -
554J LYS* 2.8 30.5 + - - +
555J HIS* 3.0 33.7 + - + +
39U GLU* 5.2 10.0 - - - +
40U GLY* 6.0 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 552 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396J CYS 2.7 19.4 + - - -
550J LYS* 3.0 42.0 + - + +
551J ASP* 1.3 79.9 - - - +
553J LEU* 1.3 75.0 + - + +
555J HIS* 4.2 7.4 - - - -
556J CYS* 3.1 26.7 + - - +
619J VAL* 3.1 41.1 - - + +
620J ALA 3.8 14.4 - - - +
621J MET 4.8 1.6 - - - +
622J GLY* 3.9 6.6 - - - -
11U GLU* 4.1 8.5 - - - -
14U ILE* 3.7 3.8 - - - +
15U PHE* 3.3 41.2 - + - -
43U GLY* 6.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393J TRP* 3.2 48.1 + - + +
396J CYS 3.4 23.8 - - - +
397J LEU* 3.6 27.6 - - + -
430J SER 4.5 5.4 - - - +
548J ARG 4.9 0.2 - - - +
550J LYS* 3.6 39.5 - - + +
551J ASP 3.0 0.4 - - - -
552J TYR* 1.3 93.9 - - + +
554J LYS* 1.3 66.6 + - - +
556J CYS* 3.2 14.9 - - - +
557J LEU* 3.2 9.7 + - - +
619J VAL* 4.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 554 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550J LYS 3.6 6.8 + - - +
551J ASP* 2.8 18.4 + - - +
553J LEU* 1.3 76.6 - - - +
555J HIS* 1.3 82.8 + - + +
556J CYS 3.1 0.9 + - - -
557J LEU* 3.2 16.6 + - - +
558J GLU* 3.1 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 555 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551J ASP* 3.0 39.5 + - + +
552J TYR* 4.1 4.3 - - - -
554J LYS* 1.3 93.5 - - + +
556J CYS* 1.3 61.7 + - - +
558J GLU* 2.9 44.6 + - - +
559J ARG* 3.3 9.2 + - - +
621J MET 5.5 1.3 - - - -
622J GLY* 2.9 36.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 556 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393J TRP* 3.4 22.2 - - + -
552J TYR 3.1 21.6 + - - +
553J LEU* 3.2 9.6 - - - +
554J LYS 3.0 0.6 - - - -
555J HIS* 1.3 78.9 - - - +
557J LEU* 1.3 62.2 + - - +
558J GLU 3.1 0.2 - - - -
559J ARG* 3.2 9.0 + - - -
560J SER* 3.1 21.8 + - - -
619J VAL* 4.0 14.1 - - + -
622J GLY 3.8 1.3 + - - -
623J ILE 3.8 18.9 - - - +
625J VAL* 3.4 33.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419I LYS* 6.3 1.3 - - - -
393J TRP* 3.7 37.0 - - + +
553J LEU 3.2 10.7 + - - +
554J LYS* 3.2 9.9 + - - +
556J CYS* 1.3 74.4 - - - +
558J GLU* 1.3 56.9 + - - +
559J ARG 3.0 5.6 + - - -
560J SER* 3.2 12.5 + - - +
561J GLU* 2.8 21.3 + - - +
563J LEU* 3.6 38.8 - - + -
564J LEU* 4.1 36.2 - - + +
569J ILE* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 558 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554J LYS* 3.1 32.7 + - + +
555J HIS* 2.9 42.3 + - - +
556J CYS 3.1 0.8 - - - -
557J LEU* 1.3 77.2 - - - +
559J ARG* 1.3 70.8 + - - +
561J GLU* 3.3 14.4 - - - +
----------------------------------------------------------
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