Contacts of the strand formed by residues 323 - 330 (chain L) in PDB entry 1DZG
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 PHE 323 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320L MET* 3.8 16.8 - - + -
321L PRO* 3.3 23.6 - - + -
322L ARG* 1.3 74.2 - - - +
324L ARG* 1.3 70.9 + - - +
325L ILE* 4.3 9.9 - - + -
373L LEU* 4.0 15.9 - - + -
374L GLU* 3.7 4.9 - - - +
375L VAL* 3.0 63.6 + - + +
408L PHE* 4.6 5.2 - + - -
410L VAL* 5.1 1.6 - - + -
426L VAL* 3.4 42.4 - - + -
429L PRO* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197L ARG* 3.4 16.3 - - - +
323L PHE* 1.3 75.6 - - - +
325L ILE* 1.3 75.5 + - - +
326L GLU* 4.6 12.5 + - + -
372L PHE* 3.5 26.4 - - + -
373L LEU 3.4 11.4 - - - +
374L GLU* 2.6 44.9 + - - +
428L ASN 4.8 5.0 - - - +
429L PRO* 5.9 0.2 - - - +
430L CYS 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L ASN* 3.2 41.1 - - + +
76L ILE 4.2 8.5 - - - +
77L PHE* 3.9 26.0 - - + -
323L PHE* 4.3 12.3 - - + -
324L ARG* 1.3 80.1 - - - +
326L GLU* 1.3 65.6 + - - +
327L ASP* 6.4 0.2 - - + -
372L PHE* 3.7 1.6 - - - -
373L LEU* 3.0 60.3 + - + +
425L ARG 4.6 4.0 - - - +
426L VAL* 4.1 17.9 - - + -
428L ASN 4.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 326 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L ASN* 5.5 4.0 - - - +
77L PHE* 5.4 0.2 - - - -
197L ARG 4.4 7.9 - - - +
324L ARG* 4.6 12.4 + - - -
325L ILE* 1.3 80.2 - - - +
327L ASP* 1.3 62.7 + - - +
370L LYS* 4.4 20.4 + - - +
371L ALA 3.5 9.9 - - - +
372L PHE* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 327 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L LYS* 3.3 37.7 + - - -
75L ASN* 4.6 3.1 - - + +
76L ILE* 3.9 3.2 - - - +
77L PHE* 3.3 44.0 + - + +
325L ILE* 6.4 0.2 - - + -
326L GLU* 1.3 75.6 - - - +
328L GLY* 1.3 69.8 + - - +
329L PHE* 3.5 15.5 - - - -
369L HIS 4.7 0.2 - - - -
370L LYS* 3.4 5.5 - - - +
371L ALA* 2.8 38.7 + - - +
401L THR* 5.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 328 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327L ASP* 1.3 82.0 + - - +
329L PHE* 1.3 65.7 + - - +
369L HIS 3.4 10.3 - - - -
370L LYS* 3.6 18.3 - - - +
398L ASN 4.6 11.7 - - - +
399L ARG* 4.8 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L PHE* 3.5 24.0 - + - -
66L LEU* 3.5 36.8 - - + -
70L LYS* 4.9 4.0 - - - -
77L PHE 4.0 11.9 - - - -
78L LEU* 4.3 7.4 - - + -
327L ASP* 3.5 28.5 - - - +
328L GLY* 1.3 76.9 - - - +
330L SER* 1.3 73.9 + - - +
331L LEU* 3.5 20.9 - - + -
334L GLN* 5.1 0.2 - - - -
368L PHE* 3.5 8.2 - - - +
369L HIS* 2.9 49.4 + + + +
397L PRO* 5.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329L PHE* 1.3 85.8 - - - +
331L LEU* 1.3 59.7 + - - +
332L LYS* 3.4 0.7 + - - +
333L GLU* 2.6 46.9 + - - +
334L GLN* 3.7 2.3 - - - +
366L ASP* 2.6 31.7 + - - -
367L ALA 3.3 7.2 - - - -
368L PHE* 4.0 11.9 - - - -
395L LEU* 5.7 0.9 - - - -
397L PRO* 4.5 21.6 - - - +
----------------------------------------------------------
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