Contacts of the strand formed by residues 65 - 68 (chain H) 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 GLY 65 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PHE* 3.8 11.4 - - - -
50H VAL 3.5 1.6 - - - +
51H LEU* 3.5 9.4 - - - -
52H SER 3.0 31.0 + - - +
63H ASP 3.5 1.4 + - - -
64H LYS* 1.3 74.7 - - - +
66H LEU* 1.3 64.5 + - - -
67H GLN 3.5 0.2 + - - -
326H ILE* 3.8 9.1 - - - +
327H PHE 3.2 14.1 - - - -
328H ASP* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H PHE* 3.4 35.9 - - + -
33H TRP* 3.7 39.0 - - + -
37H TRP* 4.2 10.3 - - + -
49H PHE* 3.6 23.1 - - + -
50H VAL 3.7 4.3 - - - +
51H LEU* 5.2 0.9 - - + -
65H GLY* 1.3 71.9 - - - -
67H GLN* 1.3 58.8 + - - +
77H LEU* 3.8 13.2 - - + -
316H LEU* 3.6 26.9 - - + -
325H THR 3.4 1.7 - - - +
326H ILE* 3.3 1.9 - - - -
327H PHE* 2.9 39.2 + - + +
330H PHE* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H PHE* 3.3 6.1 - - - -
50H VAL* 2.8 44.6 + - + +
52H SER* 3.2 28.4 + - - -
54H GLY* 4.6 2.8 - - - -
65H GLY 4.6 0.4 - - - +
66H LEU* 1.3 73.2 - - - +
68H THR* 1.3 76.9 + - - +
69H SER* 3.4 2.5 + - - -
100H GLU* 4.2 12.3 + - - -
324H GLY* 3.2 31.2 + - - +
325H THR 3.1 4.5 - - - +
326H ILE* 3.9 20.8 - - + +
87I LYS* 4.3 12.9 + - - +
303I PRO* 5.2 0.3 - - - +
304I SER* 4.7 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LYS 4.2 0.2 - - - -
49H PHE* 3.6 25.0 - - + -
67H GLN* 1.3 75.5 - - - +
69H SER* 1.3 59.0 + - - +
70H GLN 3.7 0.9 - - - -
75H TYR* 3.5 33.0 - - + -
318H LEU* 4.7 2.2 - - + -
320H GLN* 2.5 37.0 + - - +
323H SER* 3.7 1.4 + - - -
324H GLY* 2.9 45.6 + - - -
325H THR 3.1 12.4 + - - +
327H PHE* 4.5 5.2 - - + -
87I LYS* 5.7 0.2 - - - -
----------------------------------------------------------
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