Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 4ZGA
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 ASN 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PRO* 4.2 16.4 + - - +
165A PRO 3.1 9.3 + - - +
166A LEU* 3.4 19.2 - - + +
167A ILE 3.1 24.9 + - - -
351A CYS 3.7 0.6 + - - -
352A VAL* 1.3 74.6 - - - +
354A VAL* 1.3 58.5 + - - +
491A TYR 3.6 3.6 - - - -
492A GLY* 3.3 4.3 - - - -
493A SER* 3.2 11.9 + - - -
494A THR* 2.8 44.1 + - - -
495A PHE* 3.9 12.7 + - + -
516A LEU* 3.5 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 3.4 12.3 - - + +
169A PHE* 4.6 10.8 - - + -
192A LEU* 4.6 22.7 - - + -
336A VAL* 6.5 0.2 - - + -
339A LEU* 4.9 11.7 - - + -
340A MET* 4.1 26.0 - - + -
343A LEU* 4.4 7.0 - - + -
352A VAL* 4.2 16.6 - - + +
353A ASN* 1.3 75.3 - - - +
355A ILE* 1.3 78.2 + - - +
356A PHE* 4.1 3.1 - - + +
489A VAL* 3.6 3.6 - - - +
491A TYR* 2.9 39.2 + - + +
495A PHE* 3.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.4 9.6 - - + -
167A ILE 3.0 11.7 + - - +
168A ILE* 4.6 8.7 - - + -
169A PHE* 2.6 36.6 + - - +
354A VAL* 1.3 80.8 - - - +
356A PHE* 1.3 59.9 + - - +
357A VAL* 3.7 27.4 - - + -
488A PHE* 4.1 16.2 - - + -
489A VAL 3.3 8.3 - - - +
495A PHE* 3.7 29.6 - - + -
509A LEU* 6.3 1.3 - - + -
512A VAL* 5.4 2.0 - - + -
513A MET* 4.1 32.5 - - + -
516A LEU* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.3 43.5 - + + -
171A VAL* 4.1 14.4 - - + -
174A PHE* 4.0 34.1 - + - -
179A MET* 4.9 2.0 - - + -
189A ILE* 3.8 43.5 - - + -
192A LEU* 5.3 9.6 - - + -
332A ILE* 5.9 1.3 - - + -
336A VAL* 4.2 8.7 - - + -
354A VAL* 4.1 5.7 - - + +
355A ILE* 1.3 72.8 - - - +
357A VAL* 1.3 63.0 + - - +
487A VAL* 4.4 13.9 - - + -
488A PHE* 3.4 2.9 - - - -
489A VAL* 2.8 53.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.8 25.1 - - + -
169A PHE 2.9 13.7 + - - +
170A SER* 3.0 28.2 - - - -
171A VAL* 3.1 8.2 + - - +
202A MET* 3.7 17.0 - - + -
217A LEU* 4.1 19.1 - - + -
355A ILE* 3.7 16.6 - - + -
356A PHE* 1.3 79.0 - - - +
358A GLY* 1.3 70.9 + - - +
487A VAL* 3.3 12.3 - - - +
488A PHE* 4.9 4.9 - - + -
910A 4O3 4.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 6.1 0.7 - - - -
171A VAL* 3.5 14.6 - - - -
174A PHE* 4.5 1.6 - - - -
202A MET* 3.6 12.3 - - - +
217A LEU* 4.1 6.4 - - - +
357A VAL* 1.3 78.2 - - - +
359A ASP* 1.3 58.8 + - - -
486A THR* 3.2 31.0 - - - +
487A VAL* 3.0 19.2 + - - +
506A ASN* 5.8 0.3 + - - -
----------------------------------------------------------
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