Contacts of the helix formed by residues 339 - 345 (chain A) in PDB entry 5K9S
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 339 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 4.6 11.9 - - + +
302A LEU* 3.8 26.5 - - + +
303A GLY* 4.2 19.7 - - - +
335A GLY 4.7 6.5 - - - +
336A ALA 3.0 11.4 + - - +
338A ALA* 1.3 76.8 - - + +
340A PHE* 1.3 63.2 + - - +
341A PRO* 3.3 4.3 - - - -
342A SER* 2.9 26.7 + - - +
343A LEU* 3.4 25.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 4.1 15.9 - - + -
314A LEU* 4.3 11.7 - - + -
317A ILE* 4.7 4.9 - - + -
336A ALA* 3.1 37.7 - - + -
337A LEU* 3.5 11.0 + - + +
338A ALA 3.5 0.4 - - - -
339A VAL* 1.3 77.2 - - - +
341A PRO* 1.3 61.5 - - + +
343A LEU* 3.9 9.9 - - + -
344A LEU* 2.8 35.3 + - + +
355A ALA* 3.5 37.0 - - + -
358A THR* 3.6 28.5 - - + -
359A MET* 3.5 27.4 - - + -
362A ILE* 5.1 3.1 - - + -
378A LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU 3.6 9.6 - - - +
338A ALA* 3.5 13.9 - - - +
339A VAL 3.3 5.6 - - - -
340A PHE* 1.3 88.6 - - - +
342A SER* 1.3 57.7 + - - +
344A LEU* 3.6 2.5 + - + +
345A THR* 2.8 30.5 + - - +
376A HIS 5.0 4.9 - - - +
378A LEU* 3.6 18.6 - - + -
381A PHE* 3.9 38.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 2.9 28.5 + - - +
341A PRO* 1.3 75.9 - - - +
343A LEU* 1.3 61.3 + - - +
345A THR* 3.3 8.3 + - - -
346A ASN* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.9 24.7 - - + +
310A VAL* 3.8 28.5 - - + -
314A LEU* 4.4 9.9 - - + -
339A VAL* 3.6 32.3 - - + +
340A PHE* 3.2 24.8 + - + +
342A SER* 1.3 79.0 + - - +
344A LEU* 1.3 62.3 + - - +
346A ASN* 3.2 24.0 + - - +
351A ILE* 3.9 12.8 - - + +
352A GLN* 3.7 14.7 + - - -
355A ALA* 3.7 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 2.8 30.1 + - + +
341A PRO 4.0 3.4 - - - +
343A LEU* 1.3 71.1 - - - +
345A THR* 1.3 61.5 + - + +
346A ASN 3.5 0.4 - - - -
352A GLN* 3.5 20.3 + - - +
355A ALA* 4.0 10.3 - - + +
356A THR* 3.3 42.8 - - - +
359A MET* 4.4 9.0 - - + -
378A LEU* 4.5 11.2 - - + +
381A PHE* 3.9 27.4 - - + -
382A LEU* 4.3 21.1 - - + -
385A VAL* 3.6 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PRO 2.8 21.9 + - - +
342A SER* 3.3 8.5 + - - -
343A LEU 3.1 0.2 - - - -
344A LEU* 1.3 80.5 - - + +
346A ASN* 1.3 65.7 + - - +
347A PRO* 3.5 3.8 - - - +
352A GLN* 3.6 6.8 + - - +
381A PHE* 4.1 22.7 - - + +
385A VAL* 6.0 0.7 - - + -
----------------------------------------------------------
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