Contacts of the strand formed by residues 86 - 91 (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 VAL 86 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLN* 3.2 5.0 - - - +
39G GLN* 2.6 47.7 + - + +
41G PRO* 5.7 5.6 - - + -
85G ALA* 1.3 82.7 - - - +
87G TYR* 1.3 62.7 - - - +
88G TYR* 3.6 36.7 + - + +
102G GLY* 4.8 0.4 - - - -
103G THR 3.3 19.3 - - - +
104G ARG* 4.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 2.6 29.5 + - - +
21G LEU* 3.3 28.7 - - + -
36G TRP* 4.9 3.1 - - + -
37G TYR 3.3 15.5 - - - +
38G GLN* 3.0 36.5 + - + -
48G LEU* 3.4 16.6 - - + -
63G PHE* 4.1 4.7 - + - -
74G LEU* 3.8 19.1 - - + -
76G ILE* 3.8 14.9 - - + +
83G ASP* 2.7 34.0 + - - -
85G ALA 3.7 16.8 - - - -
86G VAL* 1.3 76.4 - - - +
88G TYR* 1.3 56.8 + - - +
103G THR* 2.9 24.2 + - - +
105G LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLN* 3.1 6.3 - - - +
36G TRP* 3.5 7.2 - - - -
37G TYR* 3.0 43.9 + - + +
39G GLN* 3.1 43.8 + - + -
45G PRO* 5.8 0.7 - - + -
86G VAL* 3.6 25.1 - - + +
87G TYR* 1.3 75.5 - - - +
89G CYS* 1.3 64.1 + - - +
90G GLN 4.1 0.2 + - - -
99G PHE* 4.7 5.4 - - + -
100G GLY 3.5 16.2 - - - +
101G GLN 4.3 4.0 - - - -
102G GLY* 3.4 28.7 - - - -
39H GLN* 3.4 11.7 + - - -
43H GLN 4.1 6.1 + - - -
44H GLY* 4.4 13.9 - - - -
45H LEU* 4.2 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 3.6 14.2 - - - +
6G GLN* 3.2 24.9 + - - -
23G CYS* 2.0 54.1 - - + -
34G LEU* 4.0 5.4 - - + -
35G ALA 3.1 10.1 - - - +
36G TRP* 4.1 13.2 - - + -
88G TYR* 1.3 75.4 - - - +
90G GLN* 1.3 60.7 + - - +
99G PHE* 3.1 6.3 - - - +
100G GLY* 2.9 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G LEU* 3.8 0.2 - - - -
34G LEU* 3.1 7.8 - - - +
35G ALA* 2.6 44.5 + - + +
37G TYR* 2.5 46.6 + - + -
88G TYR 4.1 0.4 + - - -
89G CYS* 1.3 75.6 - - - +
91G GLN* 1.3 63.5 + - - +
92G TYR* 4.2 5.3 - - - -
97G ILE* 3.1 33.7 - - + +
98G THR 3.5 4.3 - - - +
99G PHE* 3.7 12.6 - - + +
105H ASP 3.1 19.2 - - - +
106H ALA* 3.6 11.1 - - - +
107H MET* 3.1 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 3.6 23.1 - - + -
4G LEU* 3.5 17.5 - - + +
29G LEU* 3.9 24.2 - - + +
33G TYR 3.3 5.6 - - - +
34G LEU* 4.2 0.4 - - - -
90G GLN* 1.3 75.0 - - - +
92G TYR* 1.3 63.6 + - - +
93G ALA* 2.8 23.0 + - - +
94G ASP 3.2 14.2 + - - -
96G PRO 3.0 26.1 + - - -
97G ILE* 3.6 8.3 - - - +
98G THR* 3.0 44.6 + - - +
----------------------------------------------------------
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