Contacts of the strand formed by residues 31 - 37 (chain P) in PDB entry 1ZGL
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 SER 31 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P PRO* 4.3 1.3 - - - +
29P HIS 3.6 1.4 - - - -
30P ARG* 1.3 81.9 - - - +
32P VAL* 1.3 67.7 + - - +
33P SER* 5.5 0.2 - - - -
48P GLU* 3.0 24.2 + - - +
49P TYR 2.5 21.2 + - - -
50P PHE* 4.4 2.7 - - - -
55P ARG* 4.5 0.4 - - - -
69P GLN* 4.0 1.8 - - - +
93P ALA 4.3 0.4 - - - -
94P SER* 3.3 26.2 - - - -
95P SER* 3.2 22.4 + - - -
97P ALA* 4.2 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P CYS* 4.3 1.6 - - - +
25P PRO* 4.0 23.3 - - + -
31P SER* 1.3 82.8 + - - +
33P SER* 1.3 62.2 + - - +
34P TRP* 3.3 22.9 - - + +
48P GLU* 3.2 3.0 - - - -
49P TYR* 2.6 39.8 + - + -
69P GLN* 3.9 5.4 - - - +
73P SER 3.7 23.3 - - - +
75P SER* 4.0 16.4 - - - +
92P CYS* 3.3 28.9 - - - -
93P ALA 3.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102M TYR 4.8 2.9 - - - -
103M LYS* 6.1 0.2 - - - -
31P SER* 5.5 0.2 - - - -
32P VAL* 1.3 75.8 - - - +
34P TRP* 1.3 68.5 + - - +
35P TYR* 3.3 28.1 + - - -
45P PHE* 3.5 14.6 - - - -
47P PHE 3.1 5.4 - - - -
48P GLU* 3.7 20.9 - - - -
92P CYS* 3.4 6.4 - - - -
93P ALA* 3.2 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P GLN* 4.9 5.8 - - - -
21P LEU* 3.9 10.1 - - + -
22P SER 3.5 31.2 - - - -
23P CYS* 3.5 21.8 - - + -
32P VAL* 3.3 14.6 - - + +
33P SER* 1.3 84.1 + - - +
35P TYR* 1.3 59.3 + - - +
45P PHE* 3.8 0.2 - - - -
46P LEU* 2.6 52.1 + - + +
47P PHE* 2.8 30.4 + + + -
49P TYR* 4.6 5.1 - + - -
75P SER* 3.2 32.7 + - - -
77P MET* 3.1 52.8 - - + +
90P TYR* 4.8 5.8 - - + -
91P LEU 3.4 17.5 - - - -
92P CYS* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M LYS* 3.4 11.8 - - - +
104M LEU* 3.2 33.1 + - - +
106M PHE* 4.0 21.8 - + - -
33P SER* 3.3 21.4 + - - -
34P TRP* 1.3 72.1 - - - +
36P GLN* 1.3 60.1 + - - +
37P GLN 3.9 0.2 - - - -
43P LEU* 4.1 18.4 - - + -
44P GLN* 3.3 5.6 - - - +
45P PHE* 3.3 48.2 - + + -
46P LEU* 3.3 6.5 - - - -
89P LEU 3.8 0.2 - - - +
90P TYR* 3.4 4.7 - - - +
91P LEU* 2.6 46.5 + - + +
93P ALA* 4.8 5.6 - - + -
106P ALA* 5.9 2.0 - - + -
108P PHE* 3.6 33.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P TYR* 1.3 71.5 - - - +
37P GLN* 1.3 58.7 + - - +
38P THR* 3.3 27.4 + - - +
41P GLN* 5.5 1.7 - - - +
43P LEU* 3.5 2.1 + - - -
44P GLN* 2.7 36.5 + - - +
46P LEU* 3.1 14.8 - - + +
60P PHE* 3.3 32.6 - - + -
65P PHE* 4.2 1.4 - - - -
85P GLY 4.9 2.2 + - - -
86P ASP* 3.8 19.0 + - - +
88P ALA* 3.9 13.7 - - + +
89P LEU 4.7 0.7 - - - -
90P TYR* 3.3 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M GLN* 2.5 42.8 + - - +
89M PHE* 3.9 16.8 - - - -
35P TYR 3.9 0.8 + - - -
36P GLN* 1.3 69.7 - - - +
38P THR* 1.3 66.3 + - - +
39P PRO* 4.3 1.0 - - - +
42P GLY* 5.4 1.2 - - - -
43P LEU* 3.8 22.8 - - + +
88P ALA* 3.5 4.2 - - - +
89P LEU* 3.3 56.9 + - + +
91P LEU* 4.0 13.7 - - + +
113P ARG* 4.6 6.5 + - - +
----------------------------------------------------------
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