Contacts of the strand formed by residues 57 - 65 (chain N) in PDB entry 1JJ2
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 THR 57 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N TRP* 6.2 0.7 - - + -
55N ASP 4.1 1.5 + - - -
56N GLU* 1.3 70.5 - - - +
58N VAL* 1.3 72.6 + - - +
59N VAL* 3.6 11.2 + - + -
75N THR* 3.5 33.4 - - + +
77N ALA* 4.3 11.9 - - + -
101N ALA* 5.6 4.3 - - + -
105N ASN* 5.7 5.1 + - - -
109N SER 5.7 1.3 - - - -
110N HIS 3.0 13.2 + - - -
111N VAL* 3.2 7.7 - - - +
112N ARG 2.8 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48N ILE* 4.2 15.0 - - + -
52N ALA* 3.5 33.4 - - + -
56N GLU 4.3 6.5 - - - +
57N THR* 1.3 74.5 - - - +
59N VAL* 1.3 61.5 + - - +
60N VAL* 4.3 13.2 - - + -
74N VAL* 4.5 4.5 - - + -
75N THR 2.9 13.5 + - - +
76N VAL* 3.5 15.2 - - + -
77N ALA 2.8 27.7 + - - -
112N ARG* 3.4 9.0 - - + +
114N ILE* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N VAL* 5.7 0.7 - - + -
26N TRP* 4.2 24.9 - - + -
29N VAL* 3.8 28.7 - - + -
57N THR* 4.0 11.0 - - + +
58N VAL* 1.3 77.6 - - - +
60N VAL* 1.3 67.1 + - - +
61N PRO* 3.4 5.1 - - + +
77N ALA* 3.4 10.5 - - + +
98N LEU* 4.3 7.4 - - + -
111N VAL* 3.2 31.0 - - + -
112N ARG 2.8 11.2 + - - +
113N VAL* 3.3 10.4 - - + +
114N ILE 3.0 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41N ALA* 4.0 3.8 - - + -
43N VAL* 3.9 26.7 - - + -
48N ILE* 4.7 4.7 - - + -
58N VAL* 4.3 16.4 - - + -
59N VAL* 1.3 75.9 - - - +
61N PRO* 1.3 56.8 - - - +
62N GLY 2.7 33.4 + - - +
63N LYS 3.9 7.9 - - - +
64N VAL* 3.7 20.4 - - + -
76N VAL* 4.3 4.9 - - + -
77N ALA 2.8 9.1 + - - +
78N ALA* 3.5 25.7 - - + -
79N VAL* 3.9 2.8 + - - +
98N LEU* 4.5 4.2 - - - +
114N ILE* 3.6 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 61 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7210 A 5.9 0.2 - - + -
29N VAL* 4.2 33.4 - - + +
32N ARG* 4.0 28.5 - - + +
33N LEU* 3.7 16.1 - - + +
40N HIS* 4.1 1.6 - - - -
41N ALA* 3.4 23.2 + - + -
59N VAL* 3.4 8.5 - - + +
60N VAL* 1.3 79.5 - - + +
62N GLY* 1.3 55.6 + - - +
79N VAL* 4.9 0.4 - - + -
113N VAL* 4.1 15.3 - - + -
114N ILE 3.3 15.5 - - - +
115N ARG* 4.5 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 62 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N LEU* 4.7 0.7 - - - -
40N HIS* 4.5 7.9 - - - -
41N ALA 3.3 13.5 - - - -
60N VAL* 2.7 15.6 + - - +
61N PRO* 1.3 75.8 - - - +
63N LYS* 1.3 60.8 + - - -
78N ALA* 3.8 0.9 - - - +
79N VAL* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 63 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6580 C 4.3 15.3 + - + -
6590 A 2.8 72.2 + - - +
41N ALA 2.8 12.7 + - - +
42N GLU* 3.3 7.4 - - + -
43N VAL 3.0 23.7 + - - -
60N VAL* 3.9 3.1 - - - +
62N GLY* 1.3 74.0 - - - +
64N VAL* 1.3 66.7 + - - +
65N LEU* 4.0 9.4 + - + +
79N VAL* 5.6 0.7 - - + -
80N ASP* 3.2 40.4 + - + +
82N SER 3.8 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N VAL* 3.2 10.5 - - + +
45N LEU* 3.9 18.6 - - + -
48N ILE* 3.8 20.0 - - + -
60N VAL* 3.7 23.1 - - + -
63N LYS* 1.3 72.1 - - - +
65N LEU* 1.3 67.1 + - - +
76N VAL* 4.0 11.4 - - + -
78N ALA* 3.7 24.5 - - + -
80N ASP 3.0 6.3 + - - -
81N PHE* 3.8 12.3 - - + -
82N SER 3.1 25.6 + - - -
85N ALA* 3.3 6.8 - - + +
89N ILE* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6590 A 3.4 60.3 - - + +
6600 A 3.6 10.3 - - - +
7460 A 3.4 26.0 - - + +
42N GLU* 4.5 11.2 - - + -
43N VAL 2.5 14.3 + - - +
44N ASN* 3.1 34.0 - - - +
45N LEU* 3.3 13.9 + - - +
63N LYS* 4.0 15.5 - - + +
64N VAL* 1.3 80.9 - - - +
66N GLY* 1.3 59.0 - - - +
67N SER 3.5 1.1 - - - -
82N SER* 3.9 9.6 - - - -
85N ALA* 3.6 4.3 - - - -
----------------------------------------------------------
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