Contacts of the strand formed by residues 359 - 363 (chain A) in PDB entry 3ZG2
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 VAL 359 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.4 19.4 - - + -
90A PHE* 4.1 9.6 - - + -
103A TYR* 4.0 3.8 - - - +
356A LEU* 5.4 3.1 - - + -
358A MET* 1.3 76.9 - - - +
360A MET* 1.3 67.2 + - - +
361A ARG* 3.3 15.0 - - - +
381A ALA* 3.2 4.5 - - - +
382A CYS 2.8 39.1 + - - +
384A PRO* 4.7 9.6 - - + -
416A GLY* 5.5 1.1 - - - -
1480A HEM 3.1 57.9 - - + +
1490A UDO 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 5.9 0.9 - - + -
89A PHE* 4.0 0.9 - - - -
99A PRO* 4.1 4.3 - - - +
102A VAL* 3.4 39.2 - - + +
103A TYR* 3.3 15.2 + - + +
214A PHE* 3.4 31.2 - - + -
358A MET* 3.4 27.4 - - + -
359A VAL* 1.3 83.2 - - - +
361A ARG* 1.3 87.5 + - - +
379A ILE* 4.6 5.2 - - + -
380A ILE 3.5 5.4 - - - +
381A ALA* 3.7 13.5 - - + -
1490A UDO 2.3 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.7 27.7 + - + -
90A PHE* 4.4 7.9 - - - +
97A LEU* 3.8 36.8 + - + +
98A SER 3.1 8.7 - - - +
99A PRO* 3.9 18.4 - - - +
102A VAL* 4.0 8.1 - - - +
103A TYR* 3.8 1.6 + - - -
359A VAL* 3.3 15.6 - - - +
360A MET* 1.3 102.9 + - - +
362A MET* 1.3 60.5 + - - +
379A ILE* 3.7 10.0 - - - +
380A ILE* 2.9 40.2 + - + +
420A HIS* 3.2 37.5 - - - +
1480A HEM 3.1 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 5.7 2.0 - - - +
96A ILE 3.6 1.0 - - - +
97A LEU* 3.7 0.4 - - - -
98A SER* 2.5 30.2 + - - +
101A GLU* 3.1 43.3 - - + +
102A VAL* 4.6 2.7 - - + +
361A ARG* 1.3 74.9 - - - +
363A VAL* 1.3 56.3 + - - +
364A LYS* 2.8 23.6 + - + +
377A GLY* 3.4 36.8 - - - +
378A ASP 3.2 16.2 - - - +
379A ILE* 4.6 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE 4.0 3.8 - - - -
97A LEU* 4.1 9.6 - - + -
362A MET* 1.3 69.9 - - - +
364A LYS* 1.3 60.9 + - - +
365A ALA 2.9 24.0 - - - +
367A VAL* 4.8 1.1 - - + -
374A VAL* 3.6 33.4 - - + +
375A PRO 3.3 20.4 - - - +
376A LYS* 3.2 0.2 - - - -
377A GLY* 2.7 29.5 + - - -
378A ASP* 3.0 27.4 + - + +
380A ILE* 3.8 24.7 - - + +
----------------------------------------------------------
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