Contacts of the strand formed by residues 95 - 112 (chain F) 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 THR 95 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ASP* 6.1 1.1 - - - -
95D SER* 5.7 6.3 - - - +
91F TYR* 3.1 10.9 - - - -
92F VAL* 3.0 40.5 + - + +
94F ARG* 1.3 74.1 - - - +
96F PRO* 1.3 70.8 + - - +
97F LYS* 3.6 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F LEU* 4.5 10.1 - - + -
90F TYR 4.2 0.7 - - - +
91F TYR* 3.2 39.5 - - + +
94F ARG 3.6 3.6 - - - +
95F THR* 1.3 87.9 + - - +
97F LYS* 1.3 64.8 + - - +
98F VAL* 4.4 2.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ASN* 6.0 3.2 - - - +
88F ILE 3.6 0.9 - - - +
89F LEU* 3.4 6.1 - - - +
90F TYR* 3.0 69.0 + - + +
92F VAL* 3.9 29.1 - - + +
95F THR* 3.6 20.2 - - - +
96F PRO* 1.3 79.4 - - - +
98F VAL* 1.3 63.1 + - - +
99F GLU* 3.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F THR* 3.6 26.5 - - + -
88F ILE 3.3 5.8 - - - +
89F LEU* 3.4 25.6 - - + -
96F PRO* 5.4 2.0 - - + -
97F LYS* 1.3 73.3 - - - +
99F GLU* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ILE* 3.5 25.2 - - + +
87F THR* 3.4 4.5 - - - +
88F ILE* 2.9 34.8 + - + +
90F TYR* 3.0 35.9 + - + -
97F LYS* 3.9 4.9 + - + +
98F VAL* 1.3 75.4 - - - +
100F GLN* 1.3 64.9 + - - +
101F LEU* 4.0 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F PRO* 3.5 40.2 - - + +
86F LEU 3.9 4.0 - - - +
87F THR* 3.9 19.3 + - + +
99F GLU* 1.3 80.6 - - - +
101F LEU* 1.3 63.2 + - - +
102F SER* 3.3 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 6.1 0.2 - - - +
55E VAL* 3.5 40.2 - - + -
57E ILE* 5.4 4.7 - - + -
24F PHE* 5.5 1.1 - - + -
30F TRP* 4.6 9.2 - - + -
32F TRP* 4.8 0.9 - - + -
85F PRO* 3.1 5.9 - - - +
86F LEU 2.9 34.0 + - - +
88F ILE* 3.6 48.0 - - + -
99F GLU* 4.3 8.5 - - + +
100F GLN* 1.3 72.2 - - - +
102F SER* 1.3 59.9 + - - +
104F MET* 3.5 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 3.5 13.7 + - - -
85F PRO* 4.1 7.6 - - - -
100F GLN* 3.3 13.4 + - - -
101F LEU* 1.3 75.2 - - - +
103F ASN* 1.3 83.1 + - - +
104F MET* 3.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C THR* 3.4 33.7 - - + +
57C THR* 3.7 4.0 - - - +
58C HIS* 3.3 22.7 + - - +
83F LEU* 3.5 39.1 + - + +
84F GLU 4.1 6.5 + - - -
85F PRO* 4.4 1.8 - - - +
102F SER* 1.3 85.1 - - - +
104F MET* 1.3 58.1 + - - +
105F VAL 3.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C THR* 4.0 27.4 - - - -
58C HIS* 3.2 22.8 - - - +
61C VAL* 4.8 2.9 - - + -
24F PHE* 4.6 5.8 - - + -
30F TRP* 5.0 6.7 - - + -
39F TYR* 3.2 56.2 + - + +
41F ALA* 3.3 1.6 - - - +
84F GLU 3.0 4.0 + - - -
86F LEU* 3.8 31.0 - - + +
101F LEU* 3.5 50.3 - - + +
102F SER 3.6 8.1 - - - +
103F ASN* 1.3 74.5 - - - +
105F VAL* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 4.3 0.2 - - - -
39F TYR* 3.7 17.7 - - + -
40F TYR 3.0 29.6 - - - +
41F ALA* 4.2 2.7 - - - +
42F ASN* 3.7 7.9 - - - +
83F LEU* 3.0 7.9 - - - -
84F GLU* 2.7 46.4 + - + +
85F PRO 5.0 3.4 - - - +
86F LEU* 4.8 10.1 - - + -
103F ASN 3.9 0.2 - - - -
104F MET* 1.3 86.7 - - + +
106F VAL* 1.3 76.8 + - - +
107F LYS* 4.8 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C HIS* 3.1 38.6 - - + +
4F THR* 4.3 0.5 - - - +
17F VAL* 4.2 10.3 - - + +
42F ASN* 3.1 42.8 + - + +
43F PHE* 4.3 3.1 - - - +
44F CYS* 4.1 12.6 - - - -
80F PRO* 3.9 23.8 - - + -
82F ASP 3.8 3.4 - - - +
83F LEU* 4.5 2.2 - - + +
105F VAL* 1.3 79.9 - - - +
107F LYS* 1.3 64.7 + - - +
108F SER 3.4 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ASP* 3.1 5.4 - - + +
4F THR* 2.9 61.2 + - + +
5F ASN* 6.2 0.2 - - - +
17F VAL* 3.7 5.7 - - - +
42F ASN* 5.2 0.9 - - - +
82F ASP* 2.8 18.6 + - + +
84F GLU* 2.7 44.7 + - + +
105F VAL* 3.8 10.1 + - + +
106F VAL* 1.3 80.4 - - - +
108F SER* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ALA* 6.2 0.7 - - - -
2F LEU 3.1 14.4 - - - -
3F ASP* 4.1 11.0 - - - -
17F VAL* 4.0 3.4 - - - -
81F GLN* 2.8 27.0 + - - +
82F ASP* 2.7 48.3 + - - +
106F VAL* 3.4 10.8 - - - +
107F LYS* 1.3 79.4 - - - +
109F CYS* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LEU* 2.8 36.1 + - + +
15F CYS* 4.5 8.5 - - - -
16F CYS 4.6 0.7 - - - -
17F VAL* 4.1 15.0 - - + +
44F CYS* 2.0 52.7 - - + -
53F SER* 3.6 7.3 + - - -
78F CYS* 4.0 2.2 - - - -
79F VAL 2.7 30.1 - - - -
80F PRO* 3.2 0.7 - - - -
81F GLN* 3.8 6.5 - - - +
108F SER* 1.3 73.1 - - - +
110F LYS* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS* 6.0 1.8 - - - +
15F CYS* 3.9 3.8 - - - -
53F SER* 3.3 18.4 - - - +
55F ASP* 3.3 47.5 + - + +
78F CYS* 3.6 3.1 - - - -
79F VAL* 3.0 48.4 + - + +
80F PRO 3.6 17.4 + - - -
81F GLN* 3.6 30.5 + - + +
109F CYS* 1.3 73.3 - - - +
111F CYS* 1.3 63.0 + - - +
112F SER* 3.9 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 111 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F CYS* 3.9 16.2 - - - -
48F CYS* 2.0 53.6 - - + -
49F PRO 5.6 0.2 - - - -
52F ARG* 3.3 20.6 - - - +
53F SER* 2.8 17.1 + - - +
54F ALA* 3.9 1.4 - - - -
55F ASP* 3.2 21.9 + - - -
59F SER* 3.5 9.6 - - - -
76F PRO* 4.6 8.1 - - + -
77F CYS 2.9 4.3 - - - -
110F LYS* 1.3 72.6 - - - +
112F SER* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C CYS 4.8 0.3 - - - +
79C VAL* 3.1 33.2 - - - +
80C PRO* 3.6 31.9 + - - +
55F ASP* 3.4 24.1 + - - +
56F THR* 5.1 0.2 + - - -
58F HIS* 6.1 1.3 - - - -
59F SER* 3.6 14.0 + - - -
76F PRO* 3.5 13.0 - - - +
77F CYS 2.6 36.0 + - - -
79F VAL* 3.8 15.0 - - - +
110F LYS* 3.9 5.9 + - - -
111F CYS* 1.3 74.8 - - - +
----------------------------------------------------------
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