Contacts of the strand formed by residues 394 - 402 (chain A) in PDB entry 1ORZ
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 ASP 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 3.9 29.1 - - + +
386A THR 3.1 11.1 - - - +
387A ILE* 4.7 1.9 - - - +
392A GLY 3.9 7.4 - - - +
393A GLU* 1.3 81.5 - - - +
395A LYS* 1.3 61.3 + - - +
396A VAL* 4.2 0.6 - - - +
594A ASP* 4.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 3.6 2.7 - - - -
386A THR* 2.6 52.0 + - - +
387A ILE 4.1 4.7 - - - +
388A ASP* 3.6 44.0 + - + +
393A GLU* 3.8 12.4 + - + +
394A ASP* 1.3 78.6 - - - +
396A VAL* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LYS* 4.1 23.3 - - + +
383A GLU* 3.8 28.9 - - + +
384A ALA 3.4 13.2 - - - +
385A LEU* 3.2 18.4 - - + -
395A LYS* 1.3 78.2 - - - +
397A ILE* 1.3 75.8 + - - +
398A PRO* 3.0 14.6 - - + +
439A THR* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLY 5.6 4.3 - - - +
194A VAL* 4.1 11.2 - - + +
248A PHE* 3.3 12.6 - - + -
384A ALA* 2.9 31.9 + - + +
386A THR* 3.0 39.5 - - + +
396A VAL* 1.3 79.7 - - - +
398A PRO* 1.3 70.2 - - + +
399A GLY 3.3 0.5 + - - -
400A LEU* 3.0 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLY 4.9 3.8 - - - +
193A GLU* 3.3 37.6 - - + +
194A VAL* 2.6 33.8 + - - +
396A VAL* 3.0 15.5 - - + +
397A ILE* 1.3 88.4 - - + +
399A GLY* 1.3 56.5 + - - +
400A LEU 3.5 0.3 + - - -
443A GLY* 5.1 13.5 - - - +
446A HIS* 3.4 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.2 16.2 - - - +
213A HIS 3.5 21.5 - - - -
214A LYS* 4.3 2.5 - - - -
215A THR* 2.7 34.4 + - - +
397A ILE 3.3 0.4 + - - -
398A PRO* 1.3 72.5 - - - +
400A LEU* 1.4 58.9 + - - +
401A MET* 4.3 6.0 - - - +
446A HIS* 3.4 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 6.2 0.2 - - + -
187A LEU* 3.9 24.9 - - + -
194A VAL* 3.8 8.5 - - + -
215A THR* 3.0 40.8 - - + +
217A ILE* 4.7 12.8 - - + +
243A VAL* 5.4 7.2 - - + -
246A ALA* 6.4 0.2 - - + -
248A PHE* 4.5 11.7 - - + -
376A ILE* 5.4 3.4 - - + -
383A GLU* 3.8 3.5 - - - +
384A ALA* 3.1 26.1 + - + -
397A ILE* 3.0 44.7 + - + +
398A PRO 3.3 0.2 - - - -
399A GLY* 1.4 80.0 - - - +
401A MET* 1.4 82.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A CYS* 5.6 0.9 - - - -
214A LYS* 3.6 41.3 - - + -
215A THR 3.0 15.7 + - - +
216A ILE* 3.4 22.1 - - + -
217A ILE* 2.9 26.5 + - - +
381A ASN 5.2 0.4 - - - +
382A GLY 3.0 20.6 - - - +
383A GLU* 4.2 4.7 - - + +
384A ALA* 4.1 3.6 - - - +
399A GLY* 4.8 2.9 - - - +
400A LEU* 1.4 91.3 - - - +
402A ALA* 1.4 61.5 + - - +
432A VAL* 4.0 15.9 - - + -
436A VAL* 4.9 6.7 - - + -
439A THR* 4.0 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 4.3 2.9 - - - -
217A ILE* 3.3 28.0 - - + +
376A ILE* 3.9 24.2 - - + -
378A THR* 4.1 5.4 + - + +
382A GLY* 2.8 23.6 + - - +
400A LEU* 5.9 0.2 - - + -
401A MET* 1.4 72.4 - - - +
403A CYS* 1.4 62.5 + - - +
406A ALA 5.0 0.2 - - - -
407A ALA* 3.6 26.2 - - + +
----------------------------------------------------------
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