Contacts of the strand formed by residues 472 - 480 (chain B) in PDB entry 4ZZ7
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 THR 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 4.1 8.1 - - + -
136B PHE* 3.4 34.6 - - - +
137B GLN 3.0 15.9 - - - +
139B MET* 3.8 7.2 - - - -
165B CYS* 3.8 24.9 - - + +
242B ARG* 2.9 8.5 + - - -
468B VAL 2.7 24.2 + - - +
469B ARG* 2.8 26.0 + - - +
470B PHE 3.3 0.8 - - - -
471B TYR* 1.3 84.2 - - - +
473B LYS* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLN* 3.6 13.9 + - - -
452A TRP* 3.5 61.0 - - + +
453A LYS* 5.9 3.4 - - - +
461A HIS* 5.5 2.0 - - - +
57B ARG* 6.2 0.2 - - - +
135B GLU 3.5 0.3 - - - +
136B PHE* 4.4 2.7 - - - -
137B GLN 2.9 34.8 + - - +
138B PRO 3.3 18.6 - - - +
139B MET* 3.8 30.7 + - + +
218B LYS* 5.8 5.1 - - - +
242B ARG* 3.6 18.8 - - - +
469B ARG* 5.2 0.2 - - - +
472B THR* 1.3 74.3 - - - +
474B ARG* 1.3 64.6 + - - +
475B LYS 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY* 4.1 3.3 - - - +
447A HIS* 4.7 8.3 + - - -
448A SER* 3.7 35.0 - - - +
450A GLY 4.6 0.3 - - - +
452A TRP* 2.9 20.4 + - - -
461A HIS* 3.6 31.4 + - + +
465A PRO* 4.2 16.7 - - - +
466A ASP* 2.7 42.1 + - - +
121B GLU* 4.7 7.1 + - - -
134B SER* 3.4 26.0 + - - -
135B GLU 3.6 4.3 - - - -
136B PHE* 3.8 31.4 - - + -
469B ARG* 3.6 12.6 - - - +
472B THR 4.4 0.2 + - - -
473B LYS* 1.3 70.8 - - - +
475B LYS* 1.3 64.1 + - - +
476B THR* 4.0 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A SER 2.7 29.5 + - - +
427A ASP 3.0 9.1 + - - -
428A ASN 4.4 0.2 - - - -
429A ILE* 2.8 30.1 + - - +
431A VAL 3.4 12.3 - - - +
432A GLY 3.2 11.7 - - - +
434A VAL* 3.8 15.3 - - + -
452A TRP* 3.8 12.3 - - + -
133B TRP 4.0 0.2 - - - +
134B SER* 3.2 5.4 - - - -
135B GLU* 2.7 45.2 + - + +
137B GLN* 2.8 34.4 + - - +
474B ARG* 1.3 73.4 - - - +
476B THR* 1.3 70.6 + - - +
477B VAL* 4.1 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLY 2.9 9.7 + - - +
433A MET* 3.4 6.1 - - - +
434A VAL 2.9 25.0 + - - +
441A PRO 5.2 1.0 - - - +
443A PRO* 4.0 30.0 - - + +
447A HIS* 4.3 15.2 + - + +
448A SER 3.5 15.8 + - - -
132B SER* 3.6 20.9 - - - +
133B TRP 3.6 7.2 - - - +
134B SER* 4.7 2.3 - - - -
474B ARG* 4.0 11.6 + - - +
475B LYS* 1.3 77.3 + - - +
477B VAL* 1.3 63.2 + - - +
478B THR* 4.2 2.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A SER* 4.0 23.8 - - - +
434A VAL* 3.2 17.5 - - + +
436A ILE* 4.1 21.8 - - + -
132B SER* 2.9 20.8 + - - -
133B TRP* 3.0 61.9 + - + +
135B GLU* 4.8 5.4 - - + +
475B LYS* 4.4 14.1 - - + -
476B THR* 1.3 75.0 - - - +
478B THR* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL 2.8 9.7 + - - -
435A GLY* 3.3 3.1 - - - -
436A ILE 2.8 32.3 + - - +
438A ILE* 3.9 18.3 - - + +
441A PRO* 4.0 26.2 + - + +
442A VAL 4.7 7.4 + - - +
443A PRO* 5.1 1.7 - - - +
126B VAL* 4.8 4.5 - - + -
130B ILE* 3.6 25.6 - - + -
131B ASP 3.6 4.5 - - - +
132B SER* 3.4 13.9 + - - -
476B THR* 4.8 4.3 + - - +
477B VAL* 1.3 77.3 + - - +
479B GLN* 1.3 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA* 5.1 3.4 - - - +
436A ILE* 3.8 23.3 - - + +
129B GLY 4.1 0.3 - - - +
130B ILE* 3.4 8.5 - - - +
131B ASP* 2.8 41.2 + - + +
133B TRP* 3.6 34.7 - - + -
477B VAL 4.2 0.2 - - - -
478B THR* 1.3 74.8 - - - +
480B ARG* 1.3 63.3 + - - +
481B TRP* 3.3 40.4 + - + +
479C GLN* 5.4 9.9 + - - +
423D ARG* 4.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASN* 3.5 23.6 + - - +
267A GLN* 3.3 33.6 + - - +
436A ILE* 3.1 11.0 + - - +
437A ASN* 3.1 27.2 + - - +
438A ILE* 3.3 32.5 - - + -
128B PRO 5.5 1.0 + - - -
129B GLY 4.2 8.7 - - - +
130B ILE* 4.0 20.7 - - + +
479B GLN* 1.3 77.3 - - - +
481B TRP* 1.3 73.3 + - - +
482B PRO* 3.8 18.6 - - + +
423D ARG* 6.4 0.2 - - - +
----------------------------------------------------------
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