Contacts of the strand formed by residues 31 - 37 (chain F) in PDB entry 1U3H
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 ASN 31 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F HIS* 4.4 0.3 - - - +
30F ASN* 1.3 80.7 - - - +
32F MET* 1.3 61.6 + - - +
33F TYR* 3.4 29.9 + - + -
48F TYR* 5.9 1.6 - - + -
49F SER 2.6 23.8 - - - +
50F TYR* 3.8 10.5 - - + -
69F ARG* 3.7 0.2 - - - +
94F SER* 3.3 3.1 - - - -
95F GLY 2.8 43.6 + - - +
96F ASP 3.7 3.9 + - - -
97F ALA* 3.6 11.3 - - + -
98F GLY 3.6 1.9 + - - -
61G GLN* 3.3 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F CYS* 5.2 7.2 - - - -
25F GLN* 3.5 31.0 - - + -
31F ASN* 1.3 76.5 - - - +
33F TYR* 1.3 66.1 + - - +
48F TYR* 3.4 4.9 - - - +
49F SER 2.9 28.6 + - - +
69F ARG* 2.8 41.4 - - - +
72F GLN 3.0 15.0 - - - +
73F GLU 4.1 4.3 - - - +
74F ASN 3.4 19.3 - - - +
75F PHE* 3.4 41.1 - - + -
92F CYS* 5.3 0.9 - - - -
93F ALA 3.0 13.0 - - - +
94F SER* 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E TYR* 4.4 18.5 - - + +
31F ASN* 3.4 42.4 + - - -
32F MET* 1.3 77.0 - - - +
34F TRP* 1.3 72.8 + - - +
35F TYR* 3.5 24.2 - - + -
45F LEU* 3.9 11.0 - - + -
47F TYR 3.9 3.6 - - - -
48F TYR* 3.8 21.8 - + + -
75F PHE* 3.3 13.6 - - - -
92F CYS* 3.9 2.6 - - - -
93F ALA* 2.7 35.8 + - + -
95F GLY* 4.3 3.7 - - - -
96F ASP 4.8 1.4 + - - -
98F GLY 5.0 0.3 - - - -
99F GLY* 4.5 14.2 + - - -
106F GLN* 3.3 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F GLN* 3.8 18.2 - - + -
21F LEU* 2.9 35.9 - - + -
22F SER 4.0 3.1 - - - -
23F CYS* 3.5 20.4 - - + -
33F TYR* 1.3 77.6 - - - +
35F TYR* 1.3 63.2 + - - +
45F LEU* 4.0 1.2 - - - +
46F ILE* 3.0 30.9 + - - +
47F TYR 3.3 13.3 + - - +
75F PHE* 2.8 45.4 + + - -
76F SER 3.4 12.8 - - - -
77F LEU* 3.7 37.5 - - + -
90F TYR* 4.0 14.8 - - + -
91F PHE 2.9 40.6 - - - -
92F CYS* 3.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E GLN 4.7 4.6 + - - -
106E PHE* 3.1 39.6 - + - -
33F TYR* 3.5 25.2 - - + -
34F TRP* 1.3 81.9 - - - +
36F ARG* 1.3 64.7 + - - +
43F LEU* 3.6 30.5 - - + -
44F ARG 3.3 9.4 - - - +
45F LEU* 3.8 33.0 - - + +
46F ILE* 4.2 1.6 - - - -
90F TYR* 3.4 13.3 - - - +
91F PHE* 2.9 34.1 + - + +
93F ALA* 4.2 2.2 - - + -
106F GLN* 2.9 26.4 + - - -
108F PHE* 3.7 22.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F TYR* 1.3 79.5 - - - +
37F GLN* 1.3 62.0 + - - +
38F ASP* 2.7 39.6 + - - +
41F HIS 4.6 0.2 - - - +
42F GLY 3.4 9.8 - - - +
43F LEU* 4.7 0.7 - - - -
44F ARG* 3.4 42.3 + - + +
46F ILE* 3.5 28.9 - - + -
60F ILE* 5.5 4.8 - - - +
65F TYR* 3.0 24.4 + - - -
85F SER 3.2 26.9 + - - -
86F GLN* 3.9 3.4 - - - +
87F THR 4.5 2.0 + - - +
88F SER* 3.6 16.7 + - - +
89F VAL 3.3 7.2 - - - +
90F TYR* 3.9 13.9 - - + -
91F PHE* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E GLN* 2.8 33.1 - - - +
87E THR* 5.4 0.7 - - - +
89E PHE* 3.0 20.2 - - - -
36F ARG* 1.3 69.6 - - - +
38F ASP* 1.3 78.1 + - - +
42F GLY* 3.3 17.5 - - - +
43F LEU* 3.8 10.3 - - + +
88F SER* 3.1 11.1 + - - -
89F VAL* 2.9 16.2 + - + +
91F PHE* 2.9 36.1 - - + -
----------------------------------------------------------
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