Contacts of the strand formed by residues 92 - 99 (chain H) in PDB entry 3EO1
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 92 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 4.5 7.6 - - - +
39H GLN 3.0 22.7 - - - +
40H ALA* 3.2 16.8 - - + +
41H PRO* 4.2 5.8 - - - -
89H GLU 5.1 0.9 - - - +
90H ASP 3.0 8.9 + - - +
91H THR* 1.3 79.8 - - - +
93H VAL* 1.3 64.0 + - - +
94H TYR* 3.3 14.0 - - + -
115H LEU* 3.8 5.1 - - - -
116H VAL 3.1 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.1 2.1 - - - -
39H GLN* 2.6 49.6 + - + +
41H PRO* 6.2 0.9 - - + -
92H ALA* 1.3 74.3 - - - +
94H TYR* 1.3 62.3 + - - +
95H TYR* 3.6 38.6 + - + +
112H GLN 5.4 0.4 - - - +
113H GLY* 4.1 2.0 - - - -
114H THR 3.6 22.9 - - - +
115H LEU* 4.4 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLN* 2.5 31.4 + - - -
18H VAL* 6.1 0.9 - - + -
20H VAL* 4.8 9.2 - - + -
36H TRP* 4.3 9.9 - + + -
37H VAL 3.9 2.9 - - - -
38H ARG* 3.0 36.3 + - + -
48H MET* 3.6 27.6 - - - -
81H MET* 4.1 13.9 - - - -
83H LEU* 3.2 25.6 - - + +
90H ASP* 2.7 30.3 + - - +
92H ALA 3.3 20.0 - - - -
93H VAL* 1.3 71.8 - - - +
95H TYR* 1.3 55.4 + - - +
114H THR* 2.9 21.3 + - - +
116H VAL* 4.0 22.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
39G GLN* 4.0 5.2 + - - -
42G GLY 5.1 1.0 - - - -
43G GLN* 3.4 21.5 + - - -
44G ALA* 3.6 21.5 - - + -
45G PRO* 4.4 7.6 - - + -
6H GLN* 3.8 3.4 - - - -
36H TRP* 3.3 9.4 - - - -
37H VAL 2.7 43.8 + - - +
39H GLN* 3.5 28.6 + - + -
45H LEU* 4.8 4.3 - - + -
93H VAL* 3.6 25.8 - - + +
94H TYR* 1.3 73.3 - - - +
96H CYS* 1.3 61.0 + - - +
110H TRP* 3.6 23.1 - + + -
111H GLY 4.0 7.0 - - - -
112H GLN 3.4 21.7 + - - -
113H GLY* 3.5 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 3.8 6.6 - - - +
6H GLN* 3.6 8.6 + - + -
22H CYS* 2.0 49.1 - - - -
34H ILE* 4.0 18.2 - - - -
35H SER 3.7 5.8 - - - -
36H TRP* 3.3 27.1 - - + -
79H THR* 4.7 0.4 - - - -
95H TYR* 1.3 72.5 - - - +
97H ALA* 1.3 63.6 + - - +
110H TRP* 3.5 2.2 - - - +
111H GLY 3.0 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.0 3.4 - - - -
34H ILE* 3.5 5.7 - - - +
35H SER* 2.8 39.5 + - - +
36H TRP* 5.0 0.2 - - - +
37H VAL* 5.5 1.1 - - + +
95H TYR 4.2 0.2 - - - -
96H CYS* 1.3 76.8 - - - +
98H SER* 1.3 59.9 + - - +
107H MET* 3.9 21.8 - - + -
109H TYR 3.1 17.3 - - - +
110H TRP* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H VAL* 5.4 2.6 - - - +
4H LEU* 4.0 9.9 - - - +
32H ASN* 4.3 20.6 + - - -
33H VAL 3.6 11.0 - - - -
34H ILE* 4.4 8.1 - - - -
97H ALA* 1.3 73.5 - - - +
99H THR* 1.3 61.2 + - - +
107H MET* 3.4 14.0 - - - +
108H ASP* 3.2 16.3 + - - +
109H TYR* 2.9 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ASN* 4.0 14.7 + - - -
33H VAL* 2.9 35.7 + - + +
35H SER* 3.8 23.3 - - - +
98H SER* 1.3 78.1 + - - +
100H LEU* 1.3 63.6 + - - +
101H GLY 3.2 6.2 + - - -
102H LEU 2.8 24.3 + - - +
103H VAL 4.2 6.1 - - - +
105H ASP* 3.8 9.2 - - - +
106H ALA 3.3 11.9 - - - -
107H MET* 4.1 8.1 - - + -
108H ASP* 4.0 3.9 - - - +
----------------------------------------------------------
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