Contacts of the strand formed by residues 308 - 312 (chain B) in PDB entry 5C5B
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 ASN 308 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE 3.9 0.2 - - - +
304B THR* 3.3 6.3 - - - -
305B GLN* 3.0 35.9 + - - +
306B GLY 3.4 1.0 + - - -
307B GLY* 1.3 88.6 + - - +
309B LEU* 1.3 60.5 + - - +
310B MET* 3.8 16.6 + - + +
321B LEU* 3.4 37.1 - - + +
323B GLN 3.9 2.5 - - - -
324B ASP* 3.6 18.9 - - - +
325B LEU* 4.3 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 6.1 0.2 - - + -
302B PHE* 4.4 11.7 - - + -
303B PHE 4.0 4.9 - - - +
304B THR* 4.0 11.9 - - + -
308B ASN* 1.3 71.1 - - - +
310B MET* 1.3 62.7 + - - +
321B LEU* 3.2 3.7 - - - +
322B ILE* 2.9 42.2 + - + +
323B GLN* 2.9 22.9 + - + +
325B LEU* 3.6 18.6 - - + +
344B ILE* 3.6 30.1 - - + -
353B ILE* 4.6 1.6 - - + -
355B LEU* 4.3 15.3 - - + -
366B TRP* 3.8 32.1 - - + -
370B ILE* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.2 8.3 - - - +
303B PHE* 2.9 72.0 + - + +
305B GLN* 3.8 30.7 - - + +
308B ASN* 3.8 33.0 - - + +
309B LEU* 1.3 74.6 - - - +
311B CYS* 1.3 61.1 + - - +
312B GLN 4.3 0.2 - - - -
319B GLY 5.0 3.6 - - - +
320B GLY* 3.2 10.5 - - - +
321B LEU* 3.5 32.3 - - + -
322B ILE* 4.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.9 3.8 - - - -
300B LEU* 3.5 37.0 - - - -
301B TYR 3.3 3.1 - - - -
302B PHE* 3.5 26.9 - - + -
310B MET* 1.3 73.6 - - - +
312B GLN* 1.3 64.1 + - - +
313B PRO* 3.9 8.0 - - - +
319B GLY* 4.2 0.7 - - - -
320B GLY* 2.7 32.2 + - - +
322B ILE* 3.8 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A SER* 5.3 0.5 + - - -
17A PRO* 3.6 27.1 + - + +
18A GLN* 4.5 8.8 + - - +
21A SER* 4.7 1.0 + - - -
301B TYR* 2.9 45.7 + - + +
303B PHE* 4.2 19.5 - - + -
310B MET 4.3 0.4 - - - -
311B CYS* 1.3 73.3 - - - +
313B PRO* 1.3 76.1 - - - +
316B ALA 2.6 26.7 + - - +
317B VAL 3.5 16.6 + - - -
318B ALA 4.0 3.1 - - - +
319B GLY* 3.5 22.9 + - - +
----------------------------------------------------------
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