Contacts of the strand formed by residues 340 - 346 (chain A) in PDB entry 4FYT
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 LYS 340 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 5.5 0.6 - - - +
247A SER 2.8 24.0 + - - +
248A ASN 3.2 13.6 + - - +
249A MET 3.7 16.8 + - - -
250A LEU* 3.8 33.2 - - + -
298A VAL* 3.7 6.1 - - - -
299A LEU* 3.2 25.6 - - + +
301A ARG* 4.2 3.3 - - - +
336A TYR* 2.8 18.8 + - - -
338A LEU* 3.3 3.9 - - - +
339A PRO* 1.3 83.6 - - + +
341A SER* 1.3 60.0 + - - +
342A ASP* 2.8 35.6 + - - +
358A GLY* 2.8 25.9 + - - +
359A LEU* 4.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 3.8 1.2 - - - +
299A LEU 2.9 10.2 + - - -
300A ILE* 3.6 33.3 - - - +
301A ARG 3.6 1.2 + - - -
325A LEU* 4.7 5.6 - - - -
336A TYR* 3.7 20.2 + - - -
340A LYS* 1.3 73.0 - - - +
342A ASP* 1.3 60.5 + - - +
343A GLN* 2.8 31.2 + - - -
358A GLY* 3.9 4.8 - - - -
360A VAL* 4.2 12.3 - - - +
390A LEU* 4.2 8.6 - - - +
393A GLN* 5.1 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.0 6.9 - - - +
301A ARG* 2.7 49.5 + - - +
303A TRP* 3.1 21.0 + - + -
340A LYS* 2.8 28.2 + - - +
341A SER* 1.3 72.6 - - - +
343A GLN* 1.3 61.9 + - - +
344A ILE 4.2 0.2 - - - -
358A GLY 3.1 8.4 + - - +
359A LEU* 3.6 21.8 - - + +
360A VAL* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 4.6 0.2 - - + -
301A ARG 2.8 7.9 + - - +
302A ILE* 3.4 30.9 - - + -
303A TRP* 2.7 27.4 + - - +
321A THR* 3.6 28.7 - - + +
341A SER* 2.8 41.8 + - - +
342A ASP* 1.3 77.0 + - - +
344A ILE* 1.3 62.0 + - - +
360A VAL* 3.3 19.2 - - - +
362A TYR* 2.7 36.0 + - + +
367A LEU* 3.9 11.1 - - + +
390A LEU* 4.3 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.0 20.9 - - + -
283A ILE* 3.6 40.4 - - + -
285A SER* 4.9 1.3 - - - +
287A PHE* 3.6 31.0 - - + -
303A TRP* 3.4 21.8 - - + -
343A GLN* 1.3 76.4 - - - +
345A GLY* 1.3 61.9 - - - +
346A LEU* 3.7 6.1 - - + +
359A LEU* 3.9 12.6 - - + -
360A VAL 2.9 17.8 + - - +
361A THR* 3.4 10.7 - - + -
362A TYR* 2.8 26.7 + - - -
367A LEU* 3.7 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 3.1 23.7 - - - -
303A TRP 3.0 12.4 + - - -
304A ALA* 4.3 8.4 - - - +
305A ARG 4.9 0.2 + - - -
344A ILE* 1.3 72.3 - - - +
346A LEU* 1.3 62.7 + - - -
347A PRO* 4.0 0.9 - - - +
362A TYR* 3.3 8.3 - - - -
363A ARG 4.7 0.4 - - - -
364A GLU* 4.3 18.6 - - - +
367A LEU* 3.5 13.6 - - - +
368A LEU* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 4.7 1.8 - - - -
207A VAL* 4.1 15.9 - - + -
209A THR* 3.5 38.8 - - + +
283A ILE* 4.6 3.6 - - + -
287A PHE* 4.4 7.9 - - + -
344A ILE* 3.7 24.7 - - + +
345A GLY* 1.3 76.2 - - - +
347A PRO* 1.4 73.0 - - + +
348A ASP 3.4 15.6 + - - +
349A PHE* 4.3 12.4 - - + +
361A THR* 4.0 26.0 - - + -
362A TYR 2.8 15.2 + - - +
363A ARG* 3.9 4.5 - - - -
364A GLU* 3.5 20.7 + - - +
857A GLN* 4.8 0.9 - - - +
----------------------------------------------------------
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