Contacts of the helix formed by residues 550 - 558 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 GLU* 4.5 6.3 - - - +
145 ILE* 3.9 16.8 - - - +
395 GLU* 6.1 3.8 - - + -
396E CYS 3.6 1.2 + - - -
397E LEU 2.8 32.1 + - - +
398E LEU* 4.0 6.4 - - - +
399E PRO* 4.7 4.8 - - - +
430E SER* 5.4 1.0 + - - +
548E ARG* 2.7 36.5 + - + +
549E PRO* 1.3 73.3 - - - +
551E ASP* 1.3 64.1 + - - +
552E TYR* 3.0 42.3 + - + +
553E LEU* 3.6 28.3 + - + +
554E LYS* 3.6 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 551 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395 GLU* 3.8 31.5 - - + +
549E PRO 4.7 6.3 - - - +
550E LYS* 1.3 69.9 - - - +
552E TYR* 1.3 60.7 + - - +
553E LEU 3.0 4.7 - - - -
554E LYS* 2.8 28.7 + - - +
555E HIS* 3.0 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 552 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115 GLU* 3.2 26.7 - - - -
145 ILE* 3.6 12.1 - - + +
155 PHE* 4.5 7.6 - + - -
395 GLU* 5.5 15.7 - - + +
396E CYS* 2.7 24.3 + - + +
550E LYS* 3.0 42.1 + - + +
551E ASP* 1.3 79.0 - - - +
553E LEU* 1.3 74.7 + - + +
555E HIS* 4.1 8.5 - - - -
556E CYS* 3.1 26.3 + - - +
619E VAL* 3.1 43.8 - - + +
620E ALA* 3.8 16.8 - - - +
621E MET 4.8 1.3 - - - +
622E GLY* 3.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 553 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E TRP* 3.2 49.9 + - + +
396E CYS 3.4 23.3 - - - +
397E LEU* 3.6 26.7 - - + -
430E SER 4.5 5.8 - - - +
548E ARG 4.9 0.4 - - - +
550E LYS* 3.6 40.3 + - + +
551E ASP 3.0 0.6 - - - -
552E TYR* 1.3 94.1 - - + +
554E LYS* 1.3 66.0 + - - +
556E CYS* 3.2 15.1 - - - +
557E LEU* 3.2 9.8 + - - +
619E VAL* 4.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 554 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550E LYS 3.6 6.6 + - - +
551E ASP* 2.8 18.0 + - - +
553E LEU* 1.3 76.3 - - - +
555E HIS* 1.3 81.4 + - + +
556E CYS 3.1 0.7 + - - -
557E LEU* 3.2 16.7 + - - +
558E GLU* 3.1 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 555 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551E ASP* 3.0 38.9 + - + +
552E TYR* 4.1 3.6 - - - -
554E LYS* 1.3 94.0 - - + +
556E CYS* 1.3 61.9 - - - +
558E GLU* 2.9 44.9 + - - +
559E ARG* 3.3 8.5 + - - +
621E MET 5.6 1.1 - - - -
622E GLY* 2.8 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 556 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E TRP* 3.4 22.9 - - + -
552E TYR 3.1 21.4 + - - +
553E LEU 3.2 9.0 - - - +
554E LYS 3.0 0.2 - - - -
555E HIS* 1.3 77.5 - - - +
557E LEU* 1.3 63.4 + - - +
559E ARG* 3.2 9.2 + - - -
560E SER* 3.1 21.6 + - - -
619E VAL* 4.0 12.8 - - + -
622E GLY 4.2 1.1 - - - -
623E ILE 3.8 18.9 - - - +
625E VAL* 3.4 33.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E TRP* 3.7 37.2 - - + +
553E LEU 3.6 10.1 - - - +
554E LYS* 3.2 10.1 + - - +
556E CYS* 1.3 74.7 - - - +
558E GLU* 1.3 56.4 + - - +
559E ARG 3.0 6.0 + - - -
560E SER* 3.2 12.2 + - - +
561E GLU* 2.8 21.3 - - - +
563E LEU* 3.6 38.8 - - + -
564E LEU* 4.1 37.3 - - + +
569E ILE* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 558 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554E LYS* 3.1 31.8 - - + +
555E HIS* 2.9 42.4 + - - +
556E CYS 3.1 0.6 - - - -
557E LEU* 1.3 78.2 - - - +
559E ARG* 1.3 71.7 + - - +
561E GLU* 3.3 14.2 - - - +
----------------------------------------------------------
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