Contacts of the strand formed by residues 525 - 533 (chain E) in PDB entry 3EI4
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 GLU 525 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478E LEU* 3.8 5.9 - - - +
488E SER* 4.2 1.6 - - - +
520E GLN 3.2 4.9 - - - +
521E ILE* 3.7 1.0 - - - -
522E HIS* 2.8 42.4 + - + +
523E PRO 3.4 10.5 - - - +
524E GLN* 1.3 79.6 - - - +
526E LEU* 1.3 61.8 + - - +
527E ARG* 3.2 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 526 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469E ILE* 4.8 4.0 - - + -
476E VAL* 3.1 48.9 - - + +
478E LEU* 3.7 28.9 - - + -
488E SER* 3.5 29.1 + - - +
489E GLU 5.1 0.2 - - - -
490E TRP* 3.5 35.2 - - + +
508E VAL* 5.3 1.8 - - + -
519E LEU* 4.4 9.9 - - + +
520E GLN 3.6 5.4 - - - +
521E ILE* 4.4 19.7 - - + -
525E GLU* 1.3 71.4 - - - +
527E ARG* 1.3 61.0 + - - +
528E GLN 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 527 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519E LEU* 4.3 0.2 - - - -
520E GLN* 2.9 33.0 + - - +
522E HIS* 3.1 52.9 + - + +
525E GLU* 3.2 36.7 + - - +
526E LEU* 1.3 70.8 - - - +
528E GLN* 1.3 63.3 + - - +
529E ILE* 3.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 528 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E TRP* 3.1 39.2 - - + +
493E PRO* 4.8 9.5 - - - +
517E TYR* 3.9 12.5 - - - -
519E LEU* 3.6 21.3 - - + -
526E LEU 3.3 5.7 + - - -
527E ARG* 1.3 74.4 - - - +
529E ILE* 1.3 63.1 + - - +
530E SER 4.1 9.0 - - - +
531E HIS* 3.3 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518E TYR* 2.9 44.2 + - + +
520E GLN* 3.4 35.2 - - + +
527E ARG* 3.0 30.5 - - + +
528E GLN* 1.3 73.2 - - - +
530E SER* 1.3 61.1 + - - +
531E HIS* 5.6 0.9 - - - -
572E PRO* 4.9 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 530 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517E TYR* 3.3 5.9 - - - +
518E TYR* 2.9 51.9 + - - +
528E GLN* 3.8 6.6 + - - +
529E ILE* 1.3 81.4 - - - +
531E HIS* 1.3 68.2 + - - +
532E THR* 4.3 0.5 + - - -
572E PRO 3.9 12.2 + - - -
573E SER* 4.3 4.3 + - - -
574E PHE* 3.0 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516E LEU 3.3 6.1 - - - +
517E TYR* 4.0 17.9 - - + -
528E GLN* 3.3 23.8 - - - +
529E ILE 5.6 0.4 - - - -
530E SER* 1.3 82.9 + - - +
532E THR* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 532 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515E ALA* 3.6 2.3 - - - +
516E LEU* 3.0 34.3 + - - +
517E TYR* 6.2 0.2 - - - -
530E SER* 4.3 0.5 + - - -
531E HIS* 1.3 76.3 + - - +
533E GLU* 1.3 87.8 + - - +
534E MET* 5.6 2.7 - - - -
573E SER 4.4 1.2 + - - -
574E PHE* 2.8 44.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 533 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514E ARG* 3.9 28.5 - - + +
515E ALA* 3.8 15.7 + - - +
532E THR* 1.3 97.2 - - - +
534E MET* 1.3 73.0 + - - +
----------------------------------------------------------
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