Contacts of the helix formed by residues 84 - 93 (chain M) in PDB entry 6T9L
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 ARG 84 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 4.3 18.4 + - - +
57C TYR* 4.8 14.8 - - - +
60C ALA* 3.9 24.9 - - - +
41D VAL* 5.6 2.8 - - - +
44D GLN* 3.6 26.1 + - - +
45D VAL* 3.7 28.6 - - + +
110D GLU* 4.9 13.5 + - - -
80M VAL* 4.0 12.1 - - + -
81M SER* 2.6 31.5 + - - +
83M ASN* 1.3 88.0 - - - +
85M LEU* 1.3 58.8 + - - +
86M ALA 3.4 1.1 - - - -
87M ALA* 3.4 13.4 + - + +
88M HIS* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142K MET* 3.7 35.9 - - + -
217K ILE* 4.6 26.5 - - + -
220K LEU* 5.3 3.8 - - + -
71M ILE* 5.0 14.6 - - + +
73M CYS* 5.4 8.3 - - + -
80M VAL* 4.3 18.8 - - + -
81M SER 3.4 9.7 + - - +
82M ALA 3.2 13.9 + - - +
83M ASN 3.2 1.6 - - - -
84M ARG* 1.3 76.0 - - - +
86M ALA* 1.3 61.3 + - - +
88M HIS* 3.3 6.2 + - + -
89M LEU* 3.0 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142K MET* 3.3 25.1 + - + +
143K GLY* 5.0 1.8 - - - -
145K THR* 5.6 0.4 - - + -
220K LEU* 5.3 6.1 - - + -
231K ALA 4.9 5.8 - - - +
232K GLY 4.6 5.4 - - - +
233K TYR* 3.8 31.1 - - + +
83M ASN 4.8 1.8 - - - +
84M ARG 3.4 0.4 - - - -
85M LEU* 1.3 78.8 - - - +
87M ALA* 1.3 60.9 + - - +
89M LEU* 3.8 8.2 + - - +
90M GLN* 3.5 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 6.0 4.9 - - + -
110D GLU* 5.4 4.5 - - - +
233K TYR* 3.9 23.9 - - + +
83M ASN 4.9 1.5 + - - +
84M ARG* 3.4 17.5 + - + +
85M LEU 3.2 0.4 - - - -
86M ALA* 1.3 76.8 - - - +
88M HIS* 1.3 64.6 + - - +
89M LEU 3.4 0.2 - - - -
90M GLN* 3.7 14.2 + - - +
91M ARG* 4.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU* 4.9 0.4 + - - -
73M CYS* 4.4 9.6 - - + -
76M CYS* 3.1 27.9 - - - -
78M ARG* 3.3 43.1 + - - -
80M VAL* 3.7 29.0 - - + +
84M ARG 3.0 17.3 + - - +
85M LEU* 3.3 7.2 + - + +
87M ALA* 1.3 75.7 - - - +
89M LEU* 1.3 69.0 + - + +
90M GLN 3.2 0.2 - - - -
91M ARG* 3.1 7.7 + - + +
92M CYS* 3.1 45.3 + - + -
101M ZN 3.7 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217K ILE* 4.9 10.3 - - + -
220K LEU* 4.1 35.2 - - + +
221K THR* 4.5 13.5 - - - +
224K TRP* 4.5 7.4 - - + -
73M CYS* 4.9 9.0 - - - -
75M ASN* 6.1 0.4 - - + -
85M LEU* 3.0 39.3 + - + +
86M ALA* 4.2 5.4 - - - +
87M ALA 3.4 0.4 - - - -
88M HIS* 1.3 79.4 - - + +
90M GLN* 1.3 58.9 + - + +
91M ARG 3.2 2.4 + - - -
92M CYS* 3.6 17.0 - - - -
93M LEU* 3.4 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D HIS* 3.9 12.3 - - - -
224K TRP* 4.4 22.4 + - + +
228K GLN* 4.8 17.8 + - - +
231K ALA* 5.4 3.4 - - + +
233K TYR* 3.3 56.4 - - + +
86M ALA 3.5 10.5 + - - +
87M ALA* 3.7 10.4 + - - +
88M HIS 3.2 1.2 - - - -
89M LEU* 1.3 77.9 - - + +
91M ARG* 1.3 63.8 + - + +
94M SER* 2.9 18.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C TYR* 4.4 10.3 + - - -
61C GLU* 2.6 45.8 + - - -
64C GLU* 4.9 14.3 - - - +
65C LEU* 5.1 5.7 - - - +
103D LEU* 6.1 0.8 - - - +
106D HIS* 5.7 4.6 + - - -
87M ALA 4.3 12.5 + - - +
88M HIS* 3.1 8.9 + - - +
90M GLN* 1.3 86.8 - - + +
92M CYS* 1.3 64.2 + - - +
93M LEU 3.4 1.1 - - - -
94M SER* 3.3 12.0 + - - -
95M ARG* 3.5 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M ASN* 3.3 23.1 + - - +
76M CYS* 4.8 3.6 - - + -
88M HIS* 3.1 47.2 + - + +
89M LEU* 3.6 23.3 - - - -
91M ARG* 1.3 76.5 - - - +
93M LEU* 1.3 66.2 + - - +
95M ARG* 3.4 34.8 - - - +
101M ZN 3.9 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221K THR* 3.7 40.6 - - + +
224K TRP* 3.6 39.2 - - + -
225K LYS* 6.0 2.0 - - - -
75M ASN* 3.5 26.9 - - + +
89M LEU* 3.4 39.8 + - + +
92M CYS* 1.3 81.9 - - - +
94M SER* 1.3 56.5 + - - +
95M ARG 3.2 9.8 + - - +
----------------------------------------------------------
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