Contacts of the strand formed by residues 330 - 335 (chain A) in PDB entry 4DTZ
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 ALA 330 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 5.5 5.2 - - + -
51A TYR* 5.7 2.7 - - + -
328A ALA 3.3 1.8 + - - -
329A PRO* 1.4 83.3 - - + +
331A PHE* 1.3 61.8 + - - +
354A MET* 3.7 19.5 - - + +
355A VAL 3.2 14.8 - - - +
356A LEU* 4.7 11.0 - - + -
357A ILE* 4.3 2.2 - - - -
501A LDP 2.7 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 5.5 0.2 - - + -
62A CYS* 4.6 9.2 - - - -
330A ALA* 1.3 75.3 - - - +
332A SER* 1.3 62.4 + - - +
333A LEU* 4.4 22.0 - - + -
354A MET* 3.4 8.0 - - - +
355A VAL* 2.8 67.0 + - + +
357A ILE* 3.7 24.0 - - + -
391A LYS* 4.3 9.2 - - + -
394A GLY* 3.8 26.7 - - - -
395A ASN* 4.2 23.8 - - + -
500A HEM 3.3 35.7 - - + +
501A LDP 4.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 3.6 8.8 - - - +
70A ASN* 2.9 60.3 + - - +
72A SER* 4.0 11.3 - - - -
331A PHE* 1.3 76.2 - - - +
333A LEU* 1.4 69.4 + - - +
352A GLU* 4.5 4.0 + - - +
353A LEU 3.3 10.4 + - - -
354A MET* 3.5 19.8 - - - -
500A HEM 4.9 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.5 45.1 - - + +
62A CYS* 5.5 1.1 - - - -
67A PHE* 4.2 12.3 - - + +
68A ASP* 3.2 24.5 - - - +
69A LYS* 4.2 4.3 - - + +
70A ASN* 3.6 6.6 - - - +
331A PHE* 4.4 18.6 - - + -
332A SER* 1.4 80.8 + - - +
334A TYR* 1.3 62.3 + - - +
352A GLU* 3.3 7.8 - - - +
353A LEU* 2.8 41.7 + - + +
355A VAL* 4.1 18.4 - - + -
395A ASN* 5.7 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.2 8.1 - - - -
68A ASP* 2.7 63.7 + - + +
69A LYS 3.2 28.9 - - - -
70A ASN* 4.1 11.7 - - + +
90A TRP* 4.4 15.5 - + - -
92A HIS* 4.5 12.1 - + - -
333A LEU* 1.3 77.1 - - - +
335A ALA* 1.4 75.0 + - - +
336A LYS* 4.2 18.2 + - + +
349A LYS* 6.2 0.4 - - + -
350A GLY* 3.9 18.4 - - - +
351A ASP 3.3 10.3 - - - +
352A GLU* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG 3.6 5.8 - - - +
67A PHE* 3.7 18.0 - - + -
334A TYR* 1.4 77.2 - - - +
336A LYS* 1.3 63.5 + - - +
337A GLU 3.6 16.8 - - - +
339A THR* 4.7 1.3 - - + -
347A LEU* 4.7 10.8 - - + -
348A GLU 3.6 19.3 - - - +
349A LYS* 3.9 0.9 - - - +
350A GLY 2.7 26.5 + - - -
351A ASP 2.9 15.0 + - - +
----------------------------------------------------------
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