Contacts of the strand formed by residues 51 - 59 (chain r) in PDB entry 4PJO
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 LYS 51 (chain r).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39n CYS* 3.3 10.8 + - - -
40n GLY 3.5 15.9 - - - -
41n ILE* 3.7 15.0 - - + -
44n TYR* 3.3 42.6 - - + -
43r LEU* 4.2 15.9 - - + -
44r ILE 3.2 8.7 - - - +
45r ASN* 3.1 24.1 + - - +
49r ASN* 2.9 44.5 + - - -
50r LYS* 1.3 73.1 - - - +
52r LEU* 1.3 63.1 + - - +
53r LEU 4.0 0.2 - - - -
71r LYS 3.4 1.7 - - - +
72r GLU* 3.4 2.6 - - - -
73r MET* 2.7 43.5 + - + +
74r TRP* 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 52 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67q TYR* 4.8 6.7 - - + -
42r VAL 3.5 1.9 - - - +
43r LEU* 3.4 2.8 - - - -
44r ILE* 2.7 49.0 + - + +
46r CYS* 4.5 18.4 - - + -
50r LYS* 4.5 5.2 - - + -
51r LYS* 1.3 85.0 - - - +
53r LEU* 1.3 60.8 + - - +
54r GLY 4.0 0.6 + - - -
67r LEU* 4.2 5.6 - - + -
70r VAL* 3.8 18.2 - - + -
71r LYS 3.5 4.0 - - - -
72r GLU* 4.0 24.2 - - + +
99r MET* 3.5 31.2 - - + -
101r LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44n TYR 4.9 1.1 - - - +
46n ARG* 4.0 15.0 - - + -
47n GLU* 3.8 38.1 - - - +
41r GLN* 3.5 36.0 + - + +
42r VAL 3.1 22.4 - - - +
43r LEU* 3.9 11.4 - - + +
51r LYS 4.0 0.6 - - - -
52r LEU* 1.3 74.3 - - - +
54r GLY* 1.3 60.2 + - - +
69r ASN 3.6 2.1 - - - +
70r VAL* 3.3 2.8 - - - -
71r LYS* 2.8 42.1 + - + +
73r MET* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41r GLN* 3.3 8.3 - - - -
42r VAL* 2.9 39.5 + - - +
44r ILE* 6.3 0.2 - - - +
52r LEU* 4.0 1.4 + - - +
53r LEU* 1.3 78.6 - - - +
55r ARG* 1.3 64.2 + - - -
67r LEU* 5.2 3.7 - - - +
68r GLU 3.8 2.5 - - - -
69r ASN 3.6 12.6 - - - -
70r VAL* 4.1 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48n PHE* 3.3 31.5 - - - -
53n ASP* 3.6 12.8 + - - -
54n ALA* 4.6 6.3 - - - +
39r ASN* 2.8 58.1 + - - +
40r THR 4.2 5.2 - - - +
41r GLN* 3.5 26.2 - - + +
54r GLY* 1.3 75.7 - - - +
56r VAL* 1.3 64.7 + - - +
57r LYS* 3.9 2.7 - - + -
67r LEU* 3.2 10.1 - - - +
68r GLU* 2.9 45.6 + - + +
69r ASN* 4.3 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32r LEU* 5.3 7.4 - - + -
35r SER* 4.2 16.9 + - - +
36r VAL* 3.5 38.6 - - + +
39r ASN* 5.4 3.7 + - - +
40r THR 4.5 3.4 + - - +
42r VAL* 3.7 33.9 - - + -
55r ARG* 1.3 74.2 - - - +
57r LYS* 1.3 62.7 + - - +
58r ALA 3.6 22.9 - - - +
59r PHE* 4.6 3.6 - - + -
65r MET* 4.0 22.4 - - + -
66r VAL 3.7 3.6 - - - +
67r LEU* 3.9 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59n ARG* 3.7 26.6 - - + +
-2q SER 5.6 0.3 - - - +
76q LEU* 4.2 14.3 - - + +
77q ASP* 2.6 40.1 + - - -
80q LEU* 4.3 11.1 - - + +
36r VAL* 3.9 14.1 - - - +
39r ASN* 5.7 4.9 - - - +
55r ARG* 3.8 3.1 + - + -
56r VAL* 1.3 75.9 - - - +
58r ALA* 1.3 64.1 + - - +
66r VAL* 2.9 24.7 + - + +
68r GLU* 3.3 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2q SER 5.0 7.9 - - - +
0q SER* 4.3 7.6 - - - +
3q LEU* 4.1 11.2 - - + -
80q LEU* 4.1 28.9 - - + -
36r VAL* 4.4 6.7 - - - -
56r VAL* 3.5 6.4 - - - +
57r LYS* 1.3 81.3 - - - +
59r PHE* 1.3 67.4 + - - +
65r MET* 3.3 2.6 - - - -
66r VAL* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2q SER 4.2 1.8 - - - -
-1q GLY* 3.1 31.3 - - - -
0q SER* 2.8 25.5 + - - -
3q LEU* 3.6 5.6 - - - +
24r PHE* 4.4 11.2 - + - -
29r LEU* 3.9 22.7 - - + -
32r LEU* 3.5 30.5 - - + -
33r THR* 3.2 48.5 - - + -
36r VAL* 4.0 14.1 - - + -
56r VAL* 4.6 1.1 - - + -
58r ALA* 1.3 77.2 - - - +
60r ASP* 1.3 72.6 + - - +
64r ASN 3.0 14.6 - - - +
65r MET* 3.8 13.0 - - + -
----------------------------------------------------------
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