Contacts of the helix formed by residues 85 - 93 (chain G) in PDB entry 2X86
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 ASP 85 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLU* 2.9 22.8 + - - +
84G TRP* 1.3 73.6 - - - +
86G GLY* 1.3 57.6 + - - +
87G LYS* 2.9 12.0 + - - +
88G TYR* 2.7 35.1 + - + +
89G MET* 2.9 28.0 + - - +
139G VAL* 5.1 0.2 - - - -
34H LYS* 3.3 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G TRP 3.0 8.9 + - - -
85G ASP* 1.3 70.4 + - - +
87G LYS* 1.3 59.8 + - - +
89G MET* 4.1 1.3 - - - -
90G MET* 2.8 35.7 + - - +
139G VAL* 4.1 16.4 - - - -
33H LEU* 2.9 25.7 + - - -
34H LYS 3.3 0.8 + - - -
36H GLY* 3.9 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ASP* 2.9 8.9 + - - +
86G GLY* 1.3 76.9 - - - +
88G TYR* 1.3 63.1 + - - +
90G MET* 3.9 2.9 - - - +
91G ASP* 3.0 45.7 + - - +
32H ASN* 4.2 11.9 - - - +
33H LEU* 3.2 10.7 + - - +
34H LYS* 3.8 24.2 - - + +
52H ASP* 3.8 33.3 + - + +
54H GLU* 5.6 3.7 - - - +
55H ASP* 5.8 0.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
53G LYS* 3.0 25.5 + - - -
78G CYS* 3.6 29.6 - - + -
83G GLU* 4.6 13.7 - - + -
85G ASP* 2.7 30.2 + - + +
87G LYS* 1.3 73.7 - - - +
89G MET* 1.3 67.1 + - - +
91G ASP* 3.1 6.6 + - + +
92G ASN* 2.8 53.6 + - + +
400G NAP 3.5 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G CYS* 3.9 16.2 - - - +
80G SER 3.9 10.8 - - - +
83G GLU* 3.4 48.9 - - + +
85G ASP 2.9 15.6 + - - +
86G GLY* 3.3 8.7 + - - +
88G TYR* 1.3 80.6 - - - +
90G MET* 1.3 56.6 + - - +
92G ASN* 5.0 0.7 - - - -
93G ASN* 2.9 60.5 + - - +
139G VAL* 3.8 13.7 - - + +
140G PHE* 3.9 16.2 - - - +
143G SER* 3.6 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G GLY* 2.8 23.9 + - - +
87G LYS* 4.1 2.9 - - - +
89G MET* 1.3 74.3 - - + +
91G ASP* 1.3 58.2 + - - +
94G TYR* 3.2 27.8 + - + +
95G GLN* 2.8 29.2 + - - +
139G VAL* 5.0 4.3 - - - -
142G TYR* 4.1 21.5 - - + -
143G SER* 3.9 22.7 - - - -
146G LEU* 3.6 32.8 - - + -
33H LEU* 3.7 19.7 - - + -
50H TYR* 4.2 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 6.1 0.2 - - - +
87G LYS* 3.0 41.2 + - - +
88G TYR* 3.7 6.7 - - + +
90G MET* 1.3 76.0 - - - +
92G ASN* 1.3 60.8 + - + +
95G GLN* 3.3 19.0 - - - +
96G TYR* 2.9 31.5 + - - +
52H ASP* 5.2 4.6 - - - +
55H ASP* 4.2 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS* 2.7 29.3 + - - +
74G HIS* 5.7 0.7 + - - -
76G GLY 5.0 1.2 - - - +
77G ALA* 3.8 1.4 - - - -
78G CYS* 3.2 9.1 - - - +
88G TYR* 2.8 46.2 + - + +
89G MET* 4.4 0.7 - - - +
91G ASP* 1.3 75.4 - - + +
93G ASN* 1.3 71.9 + - - +
96G TYR* 3.1 22.8 - - - +
400G NAP 2.9 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G GLY 5.7 0.7 - - - -
77G ALA* 3.4 12.5 - - + +
78G CYS* 2.8 45.8 + - - +
89G MET* 2.9 28.6 + - - +
92G ASN* 1.3 84.8 + - - +
94G TYR* 1.3 62.8 + - - +
95G GLN 3.7 0.2 - - - -
97G SER* 2.8 32.8 + - - -
140G PHE* 4.0 8.5 - - - -
143G SER* 3.2 28.2 + - - +
144G LYS* 4.6 7.4 - - + +
147G PHE* 6.0 0.2 - - - -
----------------------------------------------------------
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