Contacts of the strand formed by residues 90 - 102 (chain P) in PDB entry 2ZJQ
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 90 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P SER* 4.5 0.4 - - - -
50P VAL* 2.6 47.3 + - + +
76P LYS* 4.5 12.1 - - + -
79P ALA* 3.5 26.0 - - + -
80P LEU* 3.8 6.1 - - + -
85P MET* 3.9 18.8 - - + -
87P GLU* 2.9 41.9 + - + +
89P ARG* 1.3 77.6 - - - +
91P PHE* 1.3 55.5 + - - +
128P VAL* 4.6 5.6 - - + -
129P ALA* 3.3 28.0 - - - +
130P GLU* 3.7 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P GLY* 4.7 4.9 - - - -
48P LYS* 3.1 26.5 - - - +
49P SER* 4.2 3.6 - - - +
50P VAL* 3.7 2.7 - - - +
89P ARG 3.4 0.6 + - - +
90P LEU* 1.3 74.9 - - - +
92P VAL* 1.3 74.3 + - - +
93P LYS* 3.1 22.4 + - + -
128P VAL* 3.5 3.9 - - - -
129P ALA* 2.9 64.4 + - + +
130P GLU 3.9 2.5 - - - -
131P LYS* 3.5 48.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P ILE* 3.9 25.6 - - + +
46P ARG* 3.9 7.2 - - - -
47P GLY* 3.3 30.7 - - - +
48P LYS 2.8 15.4 + - - +
50P VAL* 4.7 3.6 - - - -
53P ALA* 4.4 8.5 - - + -
72P LEU* 3.8 28.0 - - + -
91P PHE* 1.3 74.7 - - - +
93P LYS* 1.3 64.5 + - - +
94P GLU 4.1 8.3 - - - +
95P ALA* 4.4 1.8 - - + -
126P ILE* 3.6 21.8 - - + -
127P ILE 4.0 2.7 - - - -
128P VAL* 4.6 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P PRO 5.8 1.0 + - - -
46P ARG* 5.0 3.3 - - - +
47P GLY* 4.9 3.8 + - - -
91P PHE* 3.1 22.4 + - + -
92P VAL* 1.3 75.4 - - - +
94P GLU* 1.3 77.3 + - + +
127P ILE* 2.8 31.9 + - + +
129P ALA* 3.6 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ARG* 4.3 6.5 - - - +
92P VAL* 3.4 2.0 - - - -
93P LYS* 1.3 98.0 + - + +
95P ALA* 1.3 58.3 + - - +
96P TYR* 3.5 24.6 - - + -
125P THR 4.6 0.2 - - - +
126P ILE* 2.9 3.7 - - - +
127P ILE* 2.5 71.1 + - + +
529X U 4.8 12.7 + - - +
530X G 6.1 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P VAL* 3.5 22.0 - - + +
45P ILE* 5.3 3.4 - - + -
46P ARG* 2.6 36.0 + - - +
92P VAL* 4.4 5.8 - - + -
94P GLU* 1.3 74.4 - - - +
96P TYR* 1.3 71.0 + - - +
125P THR 3.7 9.2 - - - +
126P ILE* 3.4 20.4 - - + -
529X U 4.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P PHE* 4.3 10.6 - - - -
42P VAL* 4.0 7.9 - - - +
46P ARG* 4.8 3.4 - - - +
94P GLU* 3.5 28.3 - - + -
95P ALA* 1.3 83.2 - - - +
97P VAL* 1.3 66.7 + - - +
98P ASP* 2.9 33.9 - - - -
124P ILE* 4.0 0.7 - - - +
125P THR* 2.6 58.0 + - + +
127P ILE* 5.2 4.0 - - + +
23X G 4.8 10.9 + - - -
528X G 4.2 12.6 - - - +
529X U 3.9 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P PRO* 4.3 9.0 - - + -
38P VAL* 3.8 15.7 - - + -
39P ARG* 3.4 43.2 + - + +
42P VAL* 3.6 29.4 - - + -
96P TYR* 1.3 80.2 - - - +
98P ASP* 1.3 75.4 + - - +
122P SER* 3.3 33.0 - - - +
123P HIS 3.3 9.0 - - - +
124P ILE* 4.0 7.4 - - + -
528X G 4.3 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P PRO* 4.3 3.6 - - - -
39P ARG* 5.2 2.0 - - - +
96P TYR* 2.9 33.1 - - - -
97P VAL* 1.3 81.0 - - - +
99P ALA* 1.3 58.6 + - - +
122P SER* 3.1 6.9 - - - -
123P HIS* 2.6 46.2 + - + +
125P THR* 4.4 3.8 - - - +
23X G 3.7 21.4 + - - +
24X G 3.4 35.4 - - - +
527X C 4.8 2.2 - - - +
528X G 4.7 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P PRO* 3.3 23.1 - - + +
39P ARG* 5.7 1.2 - - - +
98P ASP* 1.3 74.5 - - - +
100P GLY* 1.3 58.1 + - - +
101P PRO 5.2 0.9 - - - +
102P THR* 6.1 0.4 - - - +
120P ARG* 5.8 3.6 - - + -
121P THR 3.3 6.3 - - - +
123P HIS* 4.4 0.9 - - - -
24X G 2.9 13.4 + - - +
25X U 2.7 38.5 - - - +
527X C 6.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P ASP 3.8 2.0 + - - -
99P ALA* 1.3 80.0 - - - +
101P PRO* 1.3 79.2 - - - +
102P THR* 4.8 0.9 + - - -
121P THR* 3.0 17.7 + - - -
122P SER* 4.0 0.8 - - - +
123P HIS* 3.6 23.3 + - - -
25X U 3.7 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 3.4 36.3 - - + -
99P ALA* 5.2 1.2 - - - +
100P GLY* 1.3 95.2 + - - +
102P THR* 1.3 68.1 + - - +
103P LEU* 4.9 10.1 - - + -
120P ARG* 5.0 0.3 - - - +
121P THR* 2.8 31.0 + - + +
25X U 5.8 0.4 - - - +
26X G 3.8 18.8 - - - +
518X A 3.9 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P GLY 4.8 0.5 + - - -
101P PRO* 1.3 78.5 + - - +
103P LEU* 1.3 68.9 + - - +
104P LYS* 3.0 53.8 + - + +
118P LYS* 4.1 16.2 - - + -
119P LYS 4.0 6.1 - - - +
120P ARG* 4.3 17.0 + - - +
121P THR* 5.4 0.2 - - - -
26X G 4.8 1.8 + - - -
1274X C 4.5 10.6 + - - -
1275X A 5.0 5.4 + - - -
----------------------------------------------------------
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