Contacts of the strand formed by residues 33 - 39 (chain H) in PDB entry 5TZ2
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 TRP 33 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASP* 4.6 7.9 + - - +
54C LEU* 3.7 28.4 - - + +
56C LYS* 3.5 25.8 - - + +
58C THR* 5.1 2.4 + - - -
32H TYR* 1.3 76.2 - - - +
34H ILE* 1.3 60.6 + - - +
50H ILE* 3.6 30.7 - - + -
51H ILE* 3.4 21.3 - - - -
52H TYR* 3.4 25.6 - + + -
57H ASP* 3.2 29.6 - - + -
59H ARG* 4.0 31.0 - - + -
98H ARG* 3.6 4.7 - - - +
99H VAL* 2.8 55.4 + - + -
105H HIS* 5.9 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.1 13.2 - - + -
22H CYS* 5.3 2.0 - - - -
27H TYR* 3.6 22.7 - - - +
29H PHE* 4.0 25.1 - - + -
32H TYR 4.2 6.3 - - - +
33H TRP* 1.3 78.9 - - - +
35H GLY* 1.3 67.9 + - - +
36H TRP* 4.4 9.5 - - - +
49H GLY 4.0 0.2 - - - +
50H ILE* 3.2 3.8 - - - -
51H ILE* 2.8 49.1 + - + +
53H PRO* 4.3 4.0 - - + -
79H ALA* 3.8 21.5 - - + -
96H CYS* 4.7 9.6 - - + -
97H ALA 3.5 11.0 - - - +
98H ARG* 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TRP 4.1 0.8 - - - -
34H ILE* 1.3 75.4 - - - +
36H TRP* 1.3 64.1 + - - -
37H VAL* 5.0 3.6 - - - -
47H TRP* 4.4 6.5 - - - -
49H GLY 3.3 7.9 - - - -
50H ILE* 3.7 12.9 - - - +
95H TYR 3.7 0.5 - - - +
96H CYS* 3.3 4.9 - - - -
97H ALA* 2.8 40.2 + - - +
99H VAL* 4.3 4.9 - - - +
107H LEU* 5.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 4.0 11.9 - - - -
20H ILE* 4.0 24.7 - - + -
21H SER 4.1 10.1 - - - -
22H CYS* 3.9 22.4 - - + -
34H ILE* 4.4 6.5 - - + +
35H GLY* 1.3 75.8 - - - -
37H VAL* 1.3 63.3 + - - +
47H TRP* 3.8 2.3 - - - +
48H MET* 2.8 45.3 + - + +
49H GLY 2.8 14.7 + - - +
70H ILE* 3.7 30.9 - - + +
79H ALA* 3.7 32.2 - - + +
80H TYR 3.6 19.4 + - - -
81H LEU* 3.7 28.5 - - + -
94H TYR* 4.7 4.9 - - + -
95H TYR 3.4 17.9 - - - -
96H CYS* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLY 5.0 3.1 - - - +
36H TRP* 1.3 80.3 - - - +
38H ARG* 1.3 64.8 + - - +
45H LEU* 4.0 25.1 - - + -
46H GLU 3.3 23.6 - - - +
47H TRP* 4.7 5.8 - - + -
48H MET* 4.3 3.4 - - - -
93H VAL 3.7 0.9 - - - +
94H TYR* 3.4 4.7 - - - +
95H TYR* 2.7 46.0 + - + +
97H ALA* 5.4 0.9 - - + -
107H LEU* 4.2 14.6 - - + -
110H TRP* 4.0 28.9 - - + -
98L PHE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H VAL* 1.3 73.7 - - - +
39H GLN* 1.3 63.8 + - - +
40H MET* 3.8 20.2 - - + +
44H GLY 3.7 0.9 - - - +
45H LEU* 3.8 0.2 - - - -
46H GLU* 2.8 80.7 + - + +
48H MET* 3.7 20.5 - - + +
64H PHE* 3.5 28.0 - - - -
89H SER* 4.2 14.9 + - - -
90H ASP* 4.5 11.7 + - - -
92H ALA* 3.7 16.8 - - + -
93H VAL 3.8 2.0 - - - -
94H TYR* 3.5 29.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 1.3 75.2 - - - +
40H MET* 1.3 65.6 + - - +
41H PRO* 3.7 1.0 - - - +
42H GLY 5.9 0.4 - - - +
43H LYS 3.5 25.1 + - - +
44H GLY 3.8 7.2 - - - +
45H LEU* 3.7 14.0 - - + +
92H ALA* 3.8 3.1 - - - -
93H VAL* 2.9 40.5 + - + +
95H TYR* 3.3 19.6 + - + -
38L GLN* 2.8 45.4 + - - +
87L TYR* 3.9 5.9 + - - -
----------------------------------------------------------
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