Contacts of the helix formed by residues 91 - 98 (chain M) in PDB entry 3EXG
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 ALA 91 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87M THR* 3.8 25.4 - - + -
88M ALA 3.9 10.3 - - - +
89M TYR 3.2 5.3 + - - -
90M ARG* 1.3 73.8 - - - +
92M HIS* 1.3 66.1 + - + +
93M GLY 3.3 2.7 - - - -
94M PHE* 3.3 5.2 + - - -
95M THR* 2.8 32.2 + - - +
123M SER 5.3 3.8 - - - +
124M MET 5.3 1.6 - - - +
126M MET* 5.5 2.7 - - + +
131M PHE* 4.1 6.1 - - + -
134M GLY* 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M MET* 4.4 13.2 - - - +
46M GLU* 3.1 36.9 + - - +
62M CYS* 4.7 4.3 - - - -
63M HIS 3.6 16.7 + - - -
64M LEU* 4.3 7.9 - - + +
65M CYS* 5.0 0.2 - - - -
89M TYR 5.3 0.6 + - - -
90M ARG 3.7 1.6 - - - -
91M ALA* 1.3 75.6 + - - +
93M GLY* 1.3 66.6 + - - +
95M THR 3.5 0.3 + - - -
96M PHE* 3.1 18.7 + - - +
105M ILE* 3.6 15.3 - - + +
109M LEU* 3.8 28.4 - - + +
123M SER* 3.0 35.5 + - - -
126M MET* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M VAL* 4.1 20.1 - - - +
65M CYS* 3.7 22.4 - - - -
72M CYS* 4.1 9.2 - - - -
90M ARG 5.0 0.6 + - - -
91M ALA 3.3 0.8 - - - -
92M HIS* 1.3 77.9 - - - +
94M PHE* 1.3 59.1 + - - +
96M PHE* 3.1 5.2 + - - +
97M THR* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71M CYS* 4.6 1.1 - - + -
72M CYS* 3.3 39.3 - - + -
75M LEU* 3.7 19.3 - - + -
76M GLU* 5.9 0.4 - - - -
85M LEU* 3.9 23.3 - - + -
87M THR* 4.3 15.7 - - + -
90M ARG 4.4 12.8 - - - -
91M ALA* 3.3 5.7 + - - +
93M GLY* 1.3 73.7 - - - +
95M THR* 1.3 68.3 + - - +
96M PHE 2.9 0.5 + - - -
97M THR* 3.1 8.2 + - - -
98M ARG* 2.9 31.4 + - + +
131M PHE* 3.9 19.7 - - + -
164M LEU* 3.3 26.9 - - + -
194M GLU* 3.5 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 95 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M ALA* 2.8 25.0 + - - +
92M HIS 3.7 5.2 - - - -
94M PHE* 1.3 71.8 - - - +
96M PHE* 1.3 56.3 + - - -
98M ARG* 3.9 3.6 + - - +
99M GLY 3.8 2.3 + - - -
100M LEU* 3.0 56.7 + - + +
105M ILE* 3.5 15.5 - - + -
126M MET* 3.5 27.0 - - + +
128M ALA* 5.1 0.7 - - - +
131M PHE* 3.3 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M MET* 3.9 28.9 - - + -
41M THR* 3.7 28.0 - - + -
42M VAL* 3.8 21.3 - - + -
45M MET* 4.7 5.2 - - + -
92M HIS 3.1 11.5 + - - +
93M GLY 3.1 7.7 + - - +
94M PHE 2.9 3.8 + - - -
95M THR* 1.3 70.1 - - - +
97M THR* 1.3 60.7 + - + +
98M ARG 2.9 4.3 - - - -
99M GLY* 2.7 27.9 + - - -
100M LEU 3.4 22.0 + - - +
101M SER* 4.6 2.0 - - - -
102M VAL* 3.7 30.5 - - + -
105M ILE* 3.6 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M MET* 4.9 11.4 - - - +
42M VAL* 4.7 1.3 - - + -
72M CYS* 3.8 41.0 + - + +
73M VAL* 4.1 13.0 - - + +
76M GLU* 3.3 37.4 + - - +
93M GLY 2.9 16.9 + - - +
94M PHE* 3.4 15.1 + - - -
96M PHE* 1.3 84.1 - - + +
98M ARG* 1.3 59.1 + - - +
99M GLY 3.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M GLU* 3.0 38.9 + - - +
79M ILE* 4.1 10.2 - - - +
80M ASN 3.3 23.4 + - - -
81M PRO* 3.4 13.1 + - - +
83M ASP 2.8 24.2 + - - -
84M HIS 4.3 0.2 - - - -
85M LEU* 4.1 17.1 - - + +
94M PHE* 2.9 20.1 + - + +
95M THR 4.0 3.8 - - - +
96M PHE 2.8 0.2 + - - -
97M THR* 1.3 77.1 - - - +
99M GLY* 1.3 59.1 + - - +
100M LEU 3.6 2.7 + - - -
128M ALA* 4.3 12.3 - - + +
129M LYS* 4.5 11.6 + - - +
130M ASN* 3.1 28.7 + - - +
131M PHE* 4.0 30.5 - - + -
----------------------------------------------------------
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