Contacts of the strand formed by residues 93 - 99 (chain H) in PDB entry 1UB6
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 ALA 93 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG* 4.1 9.6 - - + -
41H GLN 3.3 16.2 - - - +
42H ILE* 3.6 19.1 - - + +
43H PRO* 5.1 4.5 - - - -
91H ASP 3.2 8.9 + - - +
92H THR* 1.3 81.7 - - - +
94H LEU* 1.3 61.7 + - - +
95H TYR* 3.5 13.9 - - + -
111H LEU* 3.4 9.6 - - - +
112H VAL 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG* 3.1 4.0 - - - -
41H GLN* 3.0 44.9 + - + +
43H PRO* 5.7 0.2 - - - +
93H ALA* 1.3 73.1 - - - +
95H TYR* 1.3 62.7 + - - +
96H TYR* 3.5 28.3 - - + +
108H GLN 4.5 5.8 - - - +
109H GLY* 3.3 11.4 - - - +
110H THR 3.1 40.4 - - - +
111H LEU* 3.7 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 3.7 6.5 - - - +
20H LEU* 3.6 29.8 - - + -
38H TRP* 4.5 7.4 - + + -
39H VAL 3.4 6.1 - - - -
40H ARG* 2.7 39.2 + - + -
50H VAL* 4.2 13.0 - - + -
69H PHE* 4.0 10.8 - + - -
82H LEU* 4.4 6.3 - - + -
84H MET* 4.1 15.6 - - - -
91H ASP* 2.6 36.0 + - - +
93H ALA* 3.5 22.0 - - + -
94H LEU* 1.3 73.8 - - - +
96H TYR* 1.3 62.0 + - - +
109H GLY* 3.4 3.6 - - - -
110H THR* 2.8 34.9 + - + +
112H VAL* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 3.4 3.4 - - - +
38H TRP* 3.2 12.6 - - - -
39H VAL* 2.7 58.4 + - + +
41H GLN* 2.7 42.7 + - + -
47H LEU* 4.5 9.2 - - + -
94H LEU* 3.5 28.6 - - + +
95H TYR* 1.3 74.1 - - - +
97H CYS* 1.3 65.0 + - - +
106H TRP* 4.3 14.1 - + + -
107H GLY 3.4 22.7 - - - -
108H GLN 3.6 18.7 + - - -
109H GLY* 3.7 8.3 - - - -
48L SER* 3.6 13.0 + - - -
49L PRO* 3.2 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 3.8 9.5 - - + +
6H GLU* 2.6 24.4 + - + +
22H CYS* 2.0 51.1 - - + -
29H PHE* 4.3 8.3 - - - -
36H MET* 4.5 2.5 - - - -
37H SER 3.7 4.5 - - - -
38H TRP* 4.0 7.0 - - + -
80H LEU* 3.9 16.2 - - - -
96H TYR* 1.3 73.4 - - - +
98H ALA* 1.3 61.3 + - - +
106H TRP* 3.2 24.4 - - - +
107H GLY 3.3 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.3 1.1 - - - -
36H MET* 3.6 9.1 - - - +
37H SER* 2.9 49.9 + - - +
39H VAL* 4.9 14.1 - - + -
96H TYR 4.9 2.2 - - - +
97H CYS* 1.3 78.2 - - - +
99H ARG* 1.3 59.4 + - - +
100H GLY* 3.6 8.7 + - - +
104H PRO* 6.5 0.4 - - + -
105H TYR 3.3 9.4 - - - +
106H TRP* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.2 1.7 - - + +
27H ILE* 4.3 17.0 - - + +
34H TYR* 3.3 62.5 + - + -
35H ILE 4.7 1.6 - - - -
36H MET* 4.0 17.7 - - + +
98H ALA* 1.3 70.3 - - - +
100H GLY* 1.3 56.6 + - - +
101H GLN* 3.1 24.1 + - - +
103H ARG* 2.9 25.6 + - - +
104H PRO* 3.2 2.1 - - - +
105H TYR* 2.9 63.7 + - + +
----------------------------------------------------------
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