Contacts of the strand formed by residues 103 - 109 (chain Y) in PDB entry 2PKA
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 LEU 103 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X LEU* 4.0 22.4 - - + -
54X THR 3.6 11.4 - - - +
56X ALA* 3.5 6.6 - - - +
91X HIS* 2.9 32.2 + - + +
101Y HIS* 2.8 13.9 + - - +
102Y ASP* 1.3 74.3 - - - +
104Y MET* 1.3 63.1 + - - +
212Y ILE* 4.2 10.8 - - + -
229Y THR* 3.6 23.6 - - + -
231Y LEU* 4.4 4.0 - - + -
234Y TYR* 3.5 42.0 - - + -
237Y TRP* 3.7 20.2 - - + -
238Y ILE* 4.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL 3.7 0.3 - - - +
53X LEU* 3.2 8.5 - - - +
54X THR* 2.9 50.7 + - + +
55X ALA 3.5 17.9 - - - +
56X ALA* 3.7 11.4 - - - -
58X CYS 3.9 4.0 - - - +
59X LYS* 3.8 29.4 - - - +
63X TYR* 3.6 27.1 - - + +
88X ASP* 3.9 13.9 - - - +
89X PHE 3.3 14.1 - - - +
90X PRO* 3.6 11.2 - - + -
103Y LEU* 1.3 79.4 - - - +
105Y LEU* 1.3 69.4 + - - +
106Y LEU* 3.7 7.6 - - + -
237Y TRP* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X VAL* 3.9 20.2 - - + -
51X TRP* 3.9 20.2 - - + -
52X VAL 3.4 9.4 - - - +
53X LEU* 3.5 23.1 - - + -
88X ASP* 3.3 2.9 - - - -
89X PHE* 2.7 46.5 + - + +
104Y MET* 1.3 72.9 - - - +
106Y LEU* 1.3 62.6 + - - +
107Y ARG 4.1 0.7 - - - -
237Y TRP* 4.0 8.0 - - + -
238Y ILE* 3.6 25.8 - - + +
241Y THR* 3.3 35.0 - - + +
242Y ILE* 3.8 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33X ILE* 3.8 31.0 - - + -
51X TRP* 3.3 9.6 - - - -
52X VAL* 2.8 49.5 + - + +
54X THR* 4.3 5.4 - - + -
63X TYR* 4.0 24.9 - - + -
65X VAL* 4.4 12.6 - - + -
85X VAL* 4.3 13.5 - - + -
87X ALA 3.7 1.1 - - - -
88X ASP* 3.4 29.2 - - + -
104Y MET* 3.7 20.9 - - + -
105Y LEU* 1.3 76.4 - - - +
107Y ARG* 1.3 61.1 + - - +
108Y LEU* 3.6 3.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LYS* 3.8 31.4 + - - +
51X TRP* 3.6 41.5 - - + -
85X VAL* 3.5 5.0 - - - -
86X THR* 2.9 47.0 + - + +
87X ALA* 2.8 30.0 + - + +
89X PHE* 4.1 1.6 - - + -
106Y LEU* 1.3 68.5 - - - +
108Y LEU* 1.3 81.0 + - - +
109Y GLN 5.0 4.2 + - - -
111Y PRO* 5.0 6.9 - - - +
246Y PRO* 2.8 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X LEU* 4.4 16.4 - - + -
49X PRO 3.5 21.3 - - - +
50X LYS* 2.9 23.8 + - - +
51X TRP 4.4 0.9 - - - +
52X VAL* 4.0 14.8 - - + -
65X VAL* 3.9 33.0 - - + -
67X LEU* 4.7 2.5 - - + -
83X PHE* 4.0 25.6 - - + -
84X GLY 3.8 3.4 - - - +
85X VAL* 4.5 2.7 - - + +
86X THR* 3.9 1.0 - - - +
106Y LEU* 3.6 3.1 + - + +
107Y ARG* 1.3 96.1 + - - +
109Y GLN* 1.3 58.8 + - - +
110Y SER* 3.0 25.4 + - - +
112Y ALA* 4.6 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X PHE* 4.9 1.7 - - - +
84X GLY* 2.8 43.2 + - - +
85X VAL 4.2 1.8 - - - +
86X THR* 3.9 19.3 - - - +
107Y ARG* 3.6 5.8 + - - -
108Y LEU* 1.3 69.4 - - - +
110Y SER* 1.3 70.0 + - - +
----------------------------------------------------------
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