Contacts of the strand formed by residues 63 - 76 (chain G) 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 PHE 63 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLN* 4.7 1.3 - - - -
46G ARG* 3.9 22.4 - - - -
48G LEU* 4.3 15.9 - - + -
49G ILE* 4.2 16.6 - - + +
55G ARG* 3.3 25.6 + - - +
59G ILE* 3.5 27.1 - - + -
60G PRO* 3.5 20.1 + - + +
61G ASP 2.8 4.0 + - - +
62G ARG* 1.3 84.6 - - + +
64G SER* 1.3 58.9 + - - +
74G LEU* 5.4 4.9 - - + -
75G THR 4.0 1.1 - - - -
76G ILE* 3.4 48.5 - - + -
83G ASP* 3.0 29.4 - - - -
87G TYR* 4.1 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G SER* 5.6 0.4 - - - +
55G ARG* 5.2 6.3 - - - +
61G ASP 4.9 3.8 - - - -
62G ARG 4.0 4.0 + - - -
63G PHE* 1.3 74.5 - - - +
65G GLY* 1.3 63.8 + - - +
73G THR 4.0 0.5 - - - +
74G LEU* 3.7 4.7 - - - +
75G THR* 2.8 59.5 + - - +
77G SER* 5.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TRP* 5.2 2.2 - - - -
49G ILE* 4.2 16.1 - - - +
53G SER* 2.8 41.8 + - - +
64G SER* 1.3 79.4 - - - +
66G SER* 1.3 61.4 + - - -
73G THR 3.5 8.5 - - - -
74G LEU* 4.4 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TRP* 5.5 1.7 + - - +
52G ALA* 4.5 5.5 - - - +
53G SER* 3.1 15.2 + - - +
65G GLY* 1.3 76.2 - - - -
67G GLY* 1.3 62.9 + - - +
72G PHE* 3.4 6.6 - - - +
73G THR* 2.9 48.0 + - - -
75G THR* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G SER* 4.5 4.5 - - - +
52G ALA* 4.0 14.2 - - - +
53G SER* 4.5 0.4 + - - -
66G SER* 1.3 81.4 + - - +
68G SER* 1.3 64.9 + - - -
71G ASP 3.5 13.0 - - - -
72G PHE* 3.8 7.4 - - - -
73G THR* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G GLY 4.2 2.7 - - - -
31G SER* 3.9 22.4 - - - -
67G GLY* 1.3 76.0 - - - -
69G GLY* 1.3 61.1 + - - +
70G THR 2.9 9.9 + - - -
71G ASP* 3.5 14.4 + - - +
72G PHE* 3.7 13.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G SER* 3.4 11.6 - - - -
29G LEU* 2.5 47.6 + - - +
30G GLY 3.8 0.8 + - - -
68G SER* 1.3 73.8 - - - +
70G THR* 1.3 62.0 + - - -
72G PHE* 3.4 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G CYS 3.2 2.9 - - - +
24G ARG* 3.2 11.3 - - - +
25G ALA* 2.9 48.5 + - - +
26G SER 5.1 0.9 - - - +
27G GLN* 3.7 13.7 - - - +
28G SER* 3.9 9.6 - - - +
68G SER 2.9 1.6 + - - -
69G GLY* 1.3 76.8 - - - -
71G ASP* 1.3 76.2 + - - +
72G PHE* 3.6 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 5.6 3.8 - - - +
23G CYS 3.6 3.1 - - - +
24G ARG* 2.9 46.1 + - - +
67G GLY* 3.5 12.5 - - - -
68G SER 3.5 13.4 + - - +
70G THR* 1.3 86.6 + - - +
72G PHE* 1.3 63.2 + - - +
73G THR* 5.2 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G SER* 3.5 1.0 + - - -
23G CYS* 3.0 38.0 + - + +
25G ALA* 4.9 0.7 - - + -
29G LEU* 3.4 42.6 - - + -
30G GLY 3.9 7.9 - - - -
31G SER 5.1 1.6 - - - -
34G LEU* 3.7 42.4 - - + -
36G TRP* 4.0 7.4 - - + +
51G GLY 5.1 0.2 - - - -
52G ALA* 4.3 10.1 - - + -
66G SER 3.4 9.9 - - - +
67G GLY 3.8 14.8 - - - -
68G SER* 3.7 20.9 - - - -
69G GLY 3.4 17.9 - - - -
70G THR 3.6 14.1 - - - -
71G ASP* 1.3 74.9 - - - +
73G THR* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G THR* 4.8 7.6 - - + -
21G LEU 3.1 13.9 - - - +
22G SER* 4.2 12.1 - - - +
36G TRP* 4.1 5.4 - - - -
64G SER 4.0 0.7 - - - +
65G GLY* 3.5 2.6 - - - -
66G SER* 2.9 46.3 + - - -
71G ASP* 5.2 4.5 - - + -
72G PHE* 1.3 81.4 - - - +
74G LEU* 1.3 59.7 + - - +
75G THR* 4.1 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ALA 3.7 1.0 - - - +
20G THR* 3.6 0.3 - - - -
21G LEU* 2.8 59.0 + - + +
36G TRP* 3.4 54.1 - - + -
48G LEU* 4.6 4.7 - - + -
49G ILE* 3.4 30.5 - - + -
63G PHE* 5.4 2.9 - - + -
64G SER 3.7 7.9 - - - +
65G GLY* 4.4 0.7 - - - -
73G THR* 1.3 73.0 - - - +
75G THR* 1.3 65.5 + - - +
76G ILE* 4.3 10.3 + - + -
87G TYR* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G ARG* 5.3 8.5 - - - -
19G ALA 3.1 6.1 - - - -
20G THR* 3.5 28.3 - - + +
62G ARG 3.1 7.8 - - - +
63G PHE* 4.9 0.4 - - - -
64G SER* 2.8 48.4 + - - +
66G SER* 5.7 1.1 - - - +
73G THR* 4.6 9.9 - - - +
74G LEU* 1.3 81.9 - - - +
76G ILE* 1.3 62.9 + - - +
77G SER* 3.6 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU 3.7 1.7 - - - +
18G ARG* 3.2 1.1 - - - -
19G ALA* 2.7 49.3 + - + +
21G LEU* 5.4 2.9 - - + -
62G ARG* 3.4 14.8 - - - +
63G PHE* 3.4 39.9 - - + -
74G LEU* 4.8 10.1 - - + +
75G THR* 1.3 70.8 - - - +
77G SER* 1.3 64.9 + - - +
78G ARG 4.6 0.2 - - - +
79G LEU* 3.7 24.5 - - + -
83G ASP* 3.6 17.0 - - + +
87G TYR* 3.8 23.1 - - + +
105G LEU* 3.9 13.2 - - + -
----------------------------------------------------------
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