Contacts of the strand formed by residues 384 - 388 (chain B) in PDB entry 4CAA
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 384 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 4.5 18.2 - - + -
52A PHE 3.4 6.1 - - - +
53A SER* 4.0 17.9 - - - -
54A PRO* 4.2 0.2 - - - -
188A ILE* 3.9 25.6 - - + -
190A PHE* 3.9 21.1 - + + -
336A ALA* 5.6 0.2 - - + -
338A LEU* 5.1 1.3 - - + -
347A ALA* 3.8 25.6 - - + -
348A SER* 3.7 30.3 - - - -
349A ALA* 4.1 2.0 - - + -
372B MET 4.1 0.6 - - - +
373B ILE* 3.5 4.0 - - - -
374B ILE* 2.9 56.1 + - + +
382B ILE* 3.8 5.8 - - - +
383B PHE* 1.3 97.3 - + + +
385B MET* 1.3 60.5 + - - +
386B SER* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 5.6 0.9 - - - +
35A PHE* 3.8 31.0 - - + -
38A TYR* 3.8 22.4 - - + -
51A ILE* 3.4 1.6 - - - +
52A PHE* 2.8 69.3 + - + +
54A PRO* 4.0 9.1 - - + +
267A LEU* 4.8 8.7 - - + -
371B LEU* 4.8 7.6 - - + -
372B MET 3.8 5.4 - - - +
373B ILE* 3.6 31.9 - - + +
382B ILE* 4.4 5.6 - - + -
384B PHE* 1.3 72.8 - - - +
386B SER* 1.3 83.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 5.0 1.8 - - - -
50A VAL* 2.9 19.8 + - - -
51A ILE* 4.1 13.7 - - - -
293A ILE* 3.6 18.4 - - - +
338A LEU* 3.9 12.5 - - - +
371B LEU* 3.7 2.6 - - - +
372B MET* 3.0 43.1 + - - +
384B PHE 5.4 1.1 - - - -
385B MET* 1.3 86.9 - - - +
387B LYS* 1.3 63.4 + - - +
388B VAL* 4.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 3.3 30.1 - - + +
42A VAL* 4.5 7.5 - - - +
45A ALA 5.3 0.6 + - - -
46A PRO 3.0 27.1 + - - -
48A LYS 3.8 11.0 + - - +
49A ASN* 3.4 6.1 - - - +
50A VAL* 2.9 39.1 + - + +
260A MET* 3.8 15.2 - - + +
264A GLU* 3.3 15.9 + - - -
293A ILE* 4.4 0.3 - - - +
370B PHE 3.5 9.2 - - - +
371B LEU* 3.4 18.6 - - + -
372B MET* 6.0 0.2 - - - -
386B SER* 1.3 75.3 + - - +
388B VAL* 1.3 64.7 + - - +
389B THR* 3.3 33.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASN* 3.7 3.6 - - - +
208A PHE* 4.3 1.0 - - + -
291A PHE* 3.7 36.6 - - + -
293A ILE* 4.1 11.0 - - + -
369B PRO* 3.3 23.9 - - - +
370B PHE* 3.1 45.4 + - + -
372B MET* 6.0 2.7 - - + -
386B SER* 4.4 4.3 - - - +
387B LYS* 1.3 75.7 - - - +
389B THR* 1.3 61.3 + - - +
390B ASN 4.1 4.3 - - - +
391B PRO* 4.0 33.4 - - + -
----------------------------------------------------------
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