Contacts of the strand formed by residues 433 - 437 (chain J) in PDB entry 4XLN
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 GLY 433 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414J ARG* 3.5 10.5 - - - +
415J VAL* 3.2 37.1 + - - +
432J TYR* 1.3 79.1 - - - +
434J ARG* 1.3 60.5 + - - -
446J VAL* 4.0 1.1 - - - -
447J VAL 3.1 13.0 - - - -
449J SER* 3.1 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162J ARG* 4.3 2.9 - - - +
163J TYR* 3.8 41.6 + - - +
411J THR* 4.7 9.5 - - - +
412J GLY* 3.3 42.2 + - - +
413J ASP 3.9 4.9 - - - -
414J ARG* 3.1 18.8 - - - +
433J GLY* 1.3 71.0 - - - -
435J VAL* 1.3 64.4 + - - +
436J GLU* 3.8 27.7 + - - +
446J VAL* 3.4 1.7 - - - -
447J VAL* 2.9 40.2 + - + +
449J SER* 3.0 7.8 + - - +
150L ILE* 6.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409J VAL* 3.7 5.6 - - + -
411J THR* 4.1 0.3 - - - -
412J GLY* 3.0 28.1 + - - -
413J ASP* 3.1 35.9 + - - +
415J VAL* 3.6 20.0 - - + -
421J LEU* 3.6 21.1 - - + -
433J GLY 3.7 1.2 + - - -
434J ARG* 1.3 72.1 - - - +
436J GLU* 1.3 67.8 - - - +
437J VAL* 4.0 13.8 + - + -
444J VAL* 4.3 6.5 - - + -
445J ARG 3.2 17.7 - - - +
446J VAL* 4.0 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 436 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J TYR 4.8 2.6 - - - +
166J GLN* 6.0 0.3 + - - -
396J VAL* 5.4 2.8 - - - +
411J THR* 4.0 8.3 - - + -
434J ARG* 3.8 34.6 + - - +
435J VAL* 1.3 75.8 - - - +
437J VAL* 1.3 62.5 + - - +
438J ASP 3.5 2.3 + - - -
445J ARG* 2.9 68.6 + - + +
447J VAL* 3.8 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 437 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403J PHE* 4.8 4.5 - - + -
407J VAL* 4.1 11.2 - - + -
409J VAL 3.2 24.5 - - - +
410J THR 4.0 0.9 - - - -
411J THR* 3.2 39.5 + - - +
435J VAL* 4.2 10.5 - - + -
436J GLU* 1.3 72.0 - - - +
438J ASP* 1.3 67.4 + - - +
439J LEU* 4.0 7.2 + - + +
444J VAL* 3.6 27.8 - - + -
445J ARG* 5.8 0.2 - - - -
190L HIS* 3.8 18.8 - - + -
194L GLU* 4.3 10.4 - - - +
----------------------------------------------------------
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