Contacts of the strand formed by residues 327 - 333 (chain A) in PDB entry 5H15
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 ALA 327 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A HIS* 5.0 1.2 + - - -
322A LYS* 3.6 13.2 - - - +
323A SER 4.4 3.6 + - - +
325A GLU* 3.2 11.2 + - + +
326A ASN* 1.3 80.5 - - - +
328A ILE* 1.3 65.2 + - - +
329A VAL* 3.9 11.1 + - + +
355A ARG* 4.5 12.6 - - + -
356A PHE 3.4 8.1 - - - +
357A ASP* 3.7 18.4 - - - +
358A TYR* 3.3 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 3.8 31.6 - - + -
321A SER 3.7 13.9 - - - +
322A LYS* 3.8 17.3 - - + -
327A ALA* 1.3 72.3 - - - +
329A VAL* 1.3 61.8 + - - +
355A ARG* 3.3 4.5 - - - -
356A PHE* 2.8 44.5 + - + +
358A TYR* 4.0 8.5 - - + +
368A PHE* 3.8 33.9 - - + -
377A LEU* 3.9 20.0 - - + -
379A LEU* 3.9 17.3 - - + -
389A TRP* 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.8 23.8 - - + +
305A HIS* 4.0 20.4 - - + +
319A ILE 3.4 4.3 - - - +
320A LEU* 3.5 0.9 - - - -
321A SER 2.8 36.9 + - - +
325A GLU* 6.0 0.4 - - - +
327A ALA* 4.6 9.2 - - + +
328A ILE* 1.3 78.3 - - - +
330A CYS* 1.4 61.3 + - - +
331A TRP* 3.6 10.0 - - + -
352A ILE* 4.1 23.6 - - + -
354A GLY 3.9 8.7 - - - +
355A ARG* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 4.4 8.3 - - - -
318A LEU* 4.0 32.5 - - - -
319A ILE 3.2 11.0 - - - -
320A LEU* 3.7 18.8 - - + -
328A ILE 4.0 1.8 + - - -
329A VAL* 1.4 69.6 - - - +
331A TRP* 1.3 58.1 + - - +
352A ILE* 3.7 1.7 - - - +
353A LEU* 2.8 37.5 + - - -
354A GLY* 3.0 23.7 + - - +
356A PHE* 4.4 9.4 - - + -
396A PRO* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 4.5 13.5 - - + -
260A LEU* 3.6 28.3 - - + -
299A PHE* 3.8 12.3 - + - -
301A THR* 3.6 15.5 - - + -
304A ILE* 3.6 30.5 - - + +
318A LEU* 3.7 3.1 - - - +
319A ILE* 2.8 65.0 + - + +
321A SER* 3.0 19.0 + - - -
329A VAL* 3.6 17.7 - - + -
330A CYS* 1.3 74.3 - - - +
332A LYS* 1.3 79.7 + - - +
333A PRO* 3.6 19.3 - - + -
350A VAL* 3.6 24.5 - - + -
351A THR 3.2 15.7 - - - +
352A ILE* 4.0 10.1 - - + -
353A LEU* 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP 4.6 4.7 - - - +
318A LEU* 4.0 20.5 - - + +
319A ILE 5.0 0.2 - - - +
331A TRP* 1.3 84.9 - - - +
333A PRO* 1.3 79.2 - - + +
335A LYS 3.3 16.8 - - - +
336A MET* 2.9 24.6 + - - +
337A GLU 4.0 1.2 - - - -
338A ASP 2.8 30.9 + - - +
339A ASP* 5.2 0.4 - - - +
350A VAL* 3.7 0.2 - - - -
351A THR* 2.8 48.2 + - + +
353A LEU* 4.0 6.3 - - + -
41C MET* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 4.6 8.1 - - + -
262A LEU* 5.7 0.4 - - + -
299A PHE* 3.7 41.1 - - + -
317A ASP 4.8 3.8 - - - +
319A ILE* 5.0 5.6 - - + -
331A TRP* 3.6 17.4 - - + +
332A LYS* 1.3 100.8 - - + +
334A GLY* 1.3 60.2 + - - +
335A LYS 4.4 0.2 - - - +
338A ASP* 4.4 1.7 - - - +
340A ILE* 3.6 30.5 - - + +
343A ILE* 3.9 22.7 - - + +
349A ASN 4.2 0.7 - - - +
350A VAL* 4.4 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