Contacts of the strand formed by residues 317 - 321 (chain A) in PDB entry 4CH9
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 317 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 4.5 4.7 - - + -
305A VAL 3.3 10.5 - - - +
306A VAL* 4.2 17.7 - - + -
315A ARG 3.4 8.9 + - - +
316A SER* 1.3 78.7 + - - +
318A GLU* 1.3 64.8 + - - +
329A GLN* 3.4 7.2 + - - +
330A ILE* 3.0 50.4 + - + +
331A ALA 3.5 23.8 - - - +
332A GLU* 4.5 3.4 - - - +
333A LEU* 3.7 21.5 - - + +
374A TRP* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A MET 4.5 0.2 - - - -
304A ILE* 3.2 6.2 - - - +
305A VAL* 2.8 40.1 + - + +
316A SER* 3.6 1.5 - - - +
317A VAL* 1.3 74.5 - - - +
319A CYS* 1.3 62.4 + - - +
320A TYR 4.3 0.2 - - - -
327A TRP* 3.7 30.7 - - + +
328A ASP 3.4 7.2 - - - +
329A GLN* 3.1 31.4 + - - +
330A ILE* 4.6 1.1 - - - -
571A MET* 4.1 15.5 - - - +
572A SER* 3.7 18.0 + - - -
573A THR* 4.9 5.2 - - - +
575A ARG* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 3.6 40.6 - - - -
303A MET 3.3 4.5 - - - -
304A ILE* 4.3 4.7 - - + +
318A GLU* 1.3 77.0 - - - +
320A TYR* 1.3 59.9 + - - +
321A ASP* 3.9 3.6 + - - +
326A ARG 3.6 1.7 - - - +
327A TRP* 3.3 6.3 - - - -
328A ASP* 2.7 38.3 + - + +
330A ILE* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 3.4 7.3 - - - -
303A MET* 2.7 42.8 + - + +
319A CYS* 1.3 72.8 - - - +
321A ASP* 1.3 58.7 + - - +
322A PHE* 3.5 47.5 + + - -
325A ASP* 2.8 40.2 + - - +
326A ARG 3.6 21.1 - - - -
327A TRP* 3.4 51.2 - + + -
567A LEU* 3.6 33.6 - - + +
568A PRO* 4.5 2.6 - - - +
569A THR* 4.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LYS 5.1 0.9 - - - +
302A VAL* 4.1 19.1 - - + +
319A CYS* 3.9 4.1 + - - +
320A TYR* 1.3 72.2 - - - +
322A PHE* 1.3 54.0 + - - +
323A GLU* 3.2 10.6 + - - +
324A GLU* 3.0 53.0 + - + +
325A ASP* 2.8 35.3 + - - -
326A ARG 2.9 16.5 + - - +
328A ASP* 5.1 4.7 - - - +
585A LYS* 4.7 10.3 - - - +
----------------------------------------------------------
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