Contacts of the strand formed by residues 343 - 349 (chain A) in PDB entry 5TF6
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 ILE 343 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A CYS* 4.7 17.3 - - - -
332A LEU* 3.8 27.1 - - + -
333A GLN* 4.7 4.9 - - + -
338A ILE* 3.8 26.7 - - + -
339A ASN 4.1 6.1 - - - +
340A GLU* 3.2 21.1 + - + +
341A LYS 3.2 3.4 - - - +
342A ASP* 1.3 81.0 - - - +
344A ARG* 1.3 64.3 + - - +
345A LYS* 4.1 5.8 - - - +
346A ILE* 4.1 28.9 - - + -
357A ILE* 4.4 4.7 - - + -
358A ILE 4.0 5.2 - - - +
359A PHE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS 5.3 2.9 - - - +
342A ASP 3.9 0.8 + - - -
343A ILE* 1.3 78.3 - - - +
345A LYS* 1.3 71.7 + - + +
358A ILE* 2.8 34.9 + - + +
359A PHE 4.1 15.3 - - - +
360A ARG* 4.3 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 3.8 28.1 - - - +
343A ILE* 3.7 2.1 - - - +
344A ARG* 1.3 91.9 - - + +
346A ILE* 1.3 71.6 + - - +
347A LEU* 4.2 31.2 - - + +
356A ILE 3.9 0.4 - - - +
357A ILE* 3.6 0.5 - - - +
358A ILE* 2.8 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 5.7 0.2 - - - +
325A PRO* 3.6 42.1 - - + +
328A ILE* 4.1 24.7 - - + -
329A CYS* 3.7 39.0 - - + +
332A LEU* 4.1 12.1 - - + -
343A ILE* 4.1 14.1 - - + -
345A LYS* 1.3 82.4 - - - +
347A LEU* 1.3 73.7 + - - +
355A ALA* 4.9 1.6 - - + -
356A ILE 3.3 10.1 - - - +
357A ILE* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 6.2 0.9 - - + -
294A GLU* 5.8 8.1 - - + +
297A GLU* 4.8 8.1 - - + -
298A VAL* 3.9 25.4 - - + -
301A LEU* 3.7 29.8 - - + -
325A PRO* 5.1 0.2 - - - -
345A LYS* 4.2 40.2 - - + +
346A ILE* 1.3 81.1 - - - +
348A LEU* 1.3 65.2 + - - +
349A VAL* 4.1 0.2 - - - +
355A ALA* 3.3 2.6 - - - +
356A ILE* 2.8 47.9 + - + +
358A ILE* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.8 33.7 - - + +
156A THR* 3.9 25.0 + - + +
295A ARG* 5.2 1.2 + - - -
298A VAL* 3.5 19.6 - - - +
319A LEU* 5.4 2.0 - - + -
321A ASP* 5.4 1.6 - - - +
323A VAL 3.7 25.8 - - - +
325A PRO* 4.0 25.7 - - + +
328A ILE* 4.2 15.9 - - + -
346A ILE* 4.4 0.8 + - + -
347A LEU* 1.3 76.1 - - - +
349A VAL* 1.3 63.3 + - - +
350A SER* 3.8 10.8 - - - +
354A GLY 4.0 4.5 - - - +
355A ALA* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 4.8 2.7 - - - +
298A VAL* 4.1 9.6 - - + -
302A LEU* 4.2 13.7 - - + -
347A LEU 4.1 3.1 - - - +
348A LEU* 1.3 76.2 - - - +
350A SER* 1.3 64.3 + - - +
351A ASP* 3.0 20.9 - - - +
352A PHE* 3.0 33.6 + - + -
354A GLY 3.0 23.5 + - - +
355A ALA* 4.4 0.4 - - - -
356A ILE* 3.8 38.4 - - + +
390A MET* 3.9 16.8 - - + -
----------------------------------------------------------
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