Contacts of the strand formed by residues 390 - 393 (chain E) in PDB entry 4UJ3
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 HIS 390 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ARG 5.5 3.0 + - - -
355E ILE* 4.1 16.0 - - + +
356E GLU 3.4 6.1 + - - +
357E PRO* 4.1 19.2 - - + +
358E VAL* 4.3 3.8 - - - +
388E CYS* 4.2 4.3 - - - +
389E LYS* 1.3 97.7 + - + +
391E ARG* 1.3 63.0 + - - +
392E ILE* 5.1 0.2 - - + -
402E TYR* 4.0 2.4 - - - +
403E ILE* 3.1 33.3 + - + +
405E PRO* 5.0 12.6 - - + -
408E ARG* 3.4 47.5 + - + -
459E GLU* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 391 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E SER 4.0 0.2 - - - +
355E ILE* 3.6 3.1 - - - -
356E GLU* 2.8 46.7 + - + +
357E PRO 4.1 9.5 + - - -
358E VAL* 3.9 31.4 - - + +
390E HIS* 1.3 76.9 - - - +
392E ILE* 1.3 65.9 + - - +
393E LYS* 5.5 0.2 - - - +
400E TYR* 3.1 64.3 - - + +
401E TYR 3.5 14.8 - - - +
402E TYR* 3.8 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 392 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E LEU* 6.5 0.7 - - + -
344E VAL* 5.3 9.4 - - + -
353E LEU* 4.0 17.9 - - + -
354E SER 3.7 2.0 - - - -
355E ILE* 3.9 35.4 - - + -
381E LEU* 6.0 0.4 - - + -
390E HIS* 5.1 0.9 - - + -
391E ARG* 1.3 78.5 - - - +
393E LYS* 1.3 71.8 + - - +
394E LEU* 4.3 4.0 - - + +
399E ASN 4.0 0.3 - - - +
400E TYR* 3.5 6.9 - - - -
401E TYR* 2.6 54.2 + - + +
403E ILE* 3.3 37.9 - - + -
408E ARG* 5.6 2.0 - - + -
411E ILE* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352E THR 3.9 0.9 - - - +
353E LEU* 3.6 5.5 - - - +
354E SER* 2.9 48.1 + - - +
392E ILE* 1.3 78.7 - - - +
394E LEU* 1.3 63.9 + - - +
395E GLY 4.7 8.7 - - - +
399E ASN 4.1 7.2 - - - +
400E TYR* 3.8 26.0 - - + -
----------------------------------------------------------
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