Contacts of the strand formed by residues 56 - 62 (chain W) in PDB entry 2JA7
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 VAL 56 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T PRO* 5.1 6.1 - - - +
50W LEU* 3.5 40.2 - - + +
51W LEU* 4.9 11.4 - - + +
53W ASP* 2.6 36.3 + - + +
54W ARG* 4.5 4.8 - - - +
55W LYS* 1.3 69.4 - - - +
57W LEU* 1.3 61.0 + - - +
58W PHE* 3.4 23.2 - - - +
59W ALA* 4.1 6.5 - - + -
75W ILE* 4.5 0.9 - - + -
76W GLN 3.3 12.8 - - - +
77W THR* 3.6 17.3 - - + -
86W ALA* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547M LEU* 5.2 2.4 - - - +
560M ILE* 3.8 16.7 - - + +
79T TRP 5.8 0.4 - - - +
80T ARG* 3.9 45.3 - - + +
81T PRO* 4.3 24.3 - - + +
83T GLN* 5.2 6.3 - - - +
51W LEU* 6.1 0.4 - - - -
54W ARG 5.8 2.0 - - - +
55W LYS 3.5 2.7 + - - +
56W VAL* 1.3 73.3 - - - +
58W PHE* 1.3 61.3 + - - +
76W GLN* 2.5 36.8 + - + +
77W THR* 3.1 31.4 - - - +
78W THR* 3.7 13.2 - - + +
79W GLU 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547M LEU* 3.2 61.7 - - + -
551M TYR* 4.4 4.0 - - + -
556M TRP* 4.0 17.5 - + - -
560M ILE* 4.5 7.6 - - + -
51W LEU* 5.5 1.3 - - - -
56W VAL* 3.2 8.3 - - - +
57W LEU* 1.3 81.7 - - - +
59W ALA* 1.3 75.2 + - - +
60W ALA* 3.6 20.4 - - + -
74W ARG* 2.9 57.0 - - + -
75W ILE* 3.4 1.2 - - - -
76W GLN* 2.7 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547M LEU* 3.8 15.9 - - - +
47W ARG* 3.0 25.0 + - - +
50W LEU* 4.2 27.1 - - + +
51W LEU* 4.8 7.6 - - + +
56W VAL* 4.1 12.6 - - + -
58W PHE* 1.3 87.0 - - - +
60W ALA* 1.3 61.7 + - - +
73W LEU* 5.1 0.7 - - + -
74W ARG 3.1 11.9 - - - +
75W ILE* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547M LEU* 3.5 11.0 - - + +
548M ASN* 3.0 40.4 - - - +
551M TYR* 3.9 10.1 - - + -
47W ARG* 3.8 7.2 - - - +
58W PHE* 3.6 12.6 - - + -
59W ALA* 1.3 75.1 - - - +
61W TYR* 1.3 58.8 + - - +
73W LEU* 2.9 18.5 - - - +
74W ARG* 3.0 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548M ASN* 2.8 28.7 + - - +
551M TYR* 4.1 3.5 - - - -
552M TRP* 4.2 3.1 + - - -
655M PHE* 5.8 5.6 - + - -
1076N HIS* 5.0 2.1 - - - +
1077N THR* 5.8 0.9 - - + +
40W HIS* 2.5 46.3 + + - +
43W GLY* 3.2 26.9 - - - -
44W ASN* 3.1 37.8 + - - +
47W ARG* 4.0 9.6 - - + +
60W ALA* 1.3 75.1 - - - +
62W LYS* 1.3 72.9 + - - +
63W VAL* 5.5 1.3 - - + -
71W PHE* 4.0 15.5 - + + -
72W LYS 3.3 13.5 - - - +
73W LEU* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551M TYR* 3.3 58.4 + - + -
552M TRP* 3.0 52.3 + - + +
554M PRO* 5.1 8.5 - - - +
61W TYR* 1.3 82.1 - - - +
63W VAL* 1.3 59.6 + - - +
64W GLU* 3.6 30.1 + - - +
71W PHE* 3.1 7.2 - - - +
72W LYS* 3.0 32.8 + - + +
----------------------------------------------------------
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