Contacts of the strand formed by residues 304 - 309 (chain B) in PDB entry 4CY1
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 304 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ILE* 3.4 6.9 - - - +
277B GLY* 3.3 36.9 - - - -
278B SER 3.1 12.3 + - - +
281B ASN 3.5 31.2 - - - +
282B LEU 3.9 7.4 - - - +
283B VAL* 4.1 3.8 - - + +
300B HIS* 3.7 24.5 - - + -
303B VAL* 1.3 68.8 - - - +
305B ILE* 1.3 61.3 + - - +
306B SER 3.7 14.6 - - - +
307B THR* 4.0 8.5 - - + -
318B SER* 4.0 11.2 - - - -
319B ALA 3.4 13.7 - - - +
320B ALA* 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL 3.2 26.5 - - - +
49B SER* 3.7 21.3 - - - +
260B TYR* 3.7 29.8 - - + -
261B CYS 3.6 21.3 - - - +
262B ILE* 3.2 9.0 - - + -
263B PHE* 3.1 25.5 + - - -
303B VAL* 3.2 4.3 + - + -
304B VAL* 1.3 73.8 - - - +
306B SER* 1.3 63.6 + - - +
319B ALA* 3.0 15.5 + - + +
320B ALA 4.6 0.4 - - - -
321B LEU* 3.6 21.8 - - + -
592C ARG* 3.8 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER 3.9 2.5 - - - -
50B SER* 3.8 15.9 - - - -
51B VAL* 3.0 33.9 + - - +
263B PHE* 3.6 22.6 - - - +
277B GLY 5.5 0.2 - - - -
304B VAL* 3.4 1.8 - - - +
305B ILE* 1.3 87.6 - - - +
307B THR* 1.3 69.0 + - - +
318B SER* 3.3 3.6 - - - -
319B ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.4 1.5 - - - +
52B LYS* 6.1 0.3 - - - +
263B PHE* 3.3 25.2 + - - +
265B ASN* 2.8 37.3 + - - +
275B VAL* 3.9 10.4 + - - -
276B SER* 3.8 12.3 - - - -
277B GLY 3.8 17.3 - - - +
283B VAL* 4.1 14.1 - - + -
304B VAL* 4.0 12.3 - - + -
306B SER* 1.3 85.1 + - - +
308B ALA* 1.3 63.6 + - - +
316B ILE* 4.6 1.8 - - + -
317B ALA 3.1 6.3 - - - +
318B SER* 4.1 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 3.5 31.2 - - + +
52B LYS* 4.3 7.4 - - + -
53B PHE* 3.6 21.1 - - + +
265B ASN* 3.7 7.0 - - - +
307B THR* 1.3 74.4 - - - +
309B CYS* 1.3 64.5 + - - +
316B ILE* 3.3 7.5 - - - +
317B ALA* 2.8 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.6 7.5 - - - +
265B ASN* 3.6 29.8 + - + -
266B PHE 4.1 12.1 - - - +
267B SER* 3.8 29.8 - - - +
275B VAL* 3.9 15.7 - - - -
308B ALA* 1.3 76.5 - - - +
310B HIS* 1.3 68.5 + - - +
311B PRO* 3.6 3.5 - - - +
315B ILE 3.7 4.0 - - - +
316B ILE* 4.4 8.1 - - - -
----------------------------------------------------------
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