Contacts of the helix formed by residues 335 - 346 (chain I) in PDB entry 5LK5
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 ASP 335 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PRO* 3.6 39.4 - - + +
92I VAL* 4.1 3.1 - - - +
333I THR* 3.5 11.1 + - - +
334I ASN* 1.3 80.1 - - - +
336I GLU* 1.3 57.1 + - - +
337I ALA* 3.0 22.5 + - - +
338I TYR* 3.1 14.4 + - + +
339I ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I THR* 4.2 13.4 + - + +
92I VAL* 4.1 8.0 - - + +
175I ILE* 3.7 32.0 - - + +
177I ARG* 2.7 47.0 + - - +
183I GLU* 4.4 3.3 - - - +
185I LYS* 5.2 9.7 + - - +
334I ASN 4.2 0.6 + - - -
335I ASP* 1.3 70.2 + - - +
337I ALA* 1.3 68.2 + - - +
339I ALA* 3.4 5.3 + - - +
340I GLU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I ASP* 3.0 10.2 + - - +
336I GLU* 1.3 80.1 - - - +
338I TYR* 1.3 62.4 + - - +
340I GLU* 3.1 10.3 + - - +
341I GLU* 3.0 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 338 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PRO* 4.2 17.9 - - + -
21I VAL* 4.0 23.5 - - + +
24I LYS* 2.6 27.4 + - - -
331I LEU* 4.1 21.5 - - + -
333I THR* 4.0 14.8 - - - -
335I ASP* 3.1 28.4 + - + +
336I GLU 3.3 0.2 - - - -
337I ALA* 1.3 74.0 - - - +
339I ALA* 1.3 67.1 + - - +
341I GLU* 3.1 27.2 + - + +
342I PHE* 2.9 33.4 + + + +
345I GLU* 5.3 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I VAL* 3.6 31.0 - - + -
94I GLN* 3.0 23.4 + - - +
173I THR* 4.9 2.2 - - + -
175I ILE* 5.5 0.7 - - + -
331I LEU* 3.8 15.7 - - + -
333I THR* 4.1 5.2 - - + -
335I ASP 3.0 11.9 + - - +
336I GLU* 3.5 10.3 - - - +
338I TYR* 1.3 78.1 - - - +
340I GLU* 1.3 56.3 + - - +
342I PHE 3.5 0.3 + - - -
343I GLY* 2.9 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LYS* 3.6 20.8 + - - +
188I ASN* 3.1 46.5 + - - +
336I GLU 3.0 13.1 + - - +
337I ALA* 3.1 12.5 + - - +
339I ALA* 1.3 77.1 - - - +
341I GLU* 1.3 62.8 + - + +
344I ASN* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ALA* 3.0 28.3 + - - +
338I TYR* 3.4 28.7 + - + +
340I GLU* 1.3 76.3 - - + +
342I PHE* 1.3 59.0 + - - +
344I ASN* 3.1 9.3 + - - +
345I GLU* 3.0 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 342 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I LYS* 3.5 36.8 - - + -
26I GLN* 3.6 37.5 - - + -
94I GLN* 4.1 6.5 - - - -
329I ASN* 3.9 15.9 - - + -
330I PHE 4.1 3.8 - - - -
331I LEU* 3.7 40.2 - - + -
338I TYR* 2.9 26.2 + - + +
339I ALA 3.8 2.7 - - - +
341I GLU* 1.3 76.4 - - - +
343I GLY* 1.3 51.5 + - - +
345I GLU* 3.2 15.8 + - + -
346I THR* 2.7 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I GLN* 3.5 15.6 - - - +
171I LEU* 3.7 18.2 - - - -
188I ASN* 3.9 5.8 - - - -
339I ALA 2.9 11.6 + - - -
340I GLU 3.3 4.0 + - - -
341I GLU 3.2 0.2 - - - -
342I PHE* 1.3 76.0 - - - +
344I ASN* 1.3 56.7 + - - +
346I THR* 3.6 5.8 - - - -
347I TRP* 3.2 15.1 + - - +
348I GLY 3.1 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 344 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ASN* 3.0 21.6 + - - +
340I GLU* 3.1 24.8 + - - +
341I GLU* 3.1 9.0 + - - +
343I GLY* 1.3 77.1 - - - +
345I GLU* 1.3 60.2 + - + +
347I TRP* 4.1 12.8 - - - -
348I GLY* 3.4 25.7 - - - -
349I VAL* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 345 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I TYR* 5.3 5.4 + - - -
341I GLU* 3.0 27.0 + - - +
342I PHE* 3.2 21.4 + - + +
344I ASN* 1.3 76.9 - - + +
346I THR* 1.3 63.6 + - + +
349I VAL* 3.4 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 346 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I GLN* 3.9 6.3 - - - +
171I LEU* 4.8 3.6 - - - +
329I ASN* 3.4 43.1 - - - +
342I PHE* 2.7 47.8 + - + +
343I GLY* 3.3 8.6 + - - -
345I GLU* 1.3 81.2 - - + +
347I TRP* 1.3 72.9 + - - +
348I GLY 3.2 0.2 - - - -
349I VAL* 3.0 13.5 + - - +
350I THR* 3.0 19.1 + - - -
----------------------------------------------------------
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