Contacts of the helix formed by residues 85 - 103 (chain B) in PDB entry 4MXR
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 THR 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 5.0 3.8 - - - -
33B GLU* 5.6 1.3 - - - -
83B ALA* 3.8 3.4 - - - +
84B SER* 1.3 88.8 + - - +
86B LEU* 1.3 64.2 + - - +
87B GLU* 4.0 11.0 + - - +
88B GLU* 3.2 26.9 + - - +
89B ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 4.1 3.8 - - + -
31B TYR* 3.6 33.0 - - + -
33B GLU* 3.9 31.8 + - + +
34B GLY* 3.5 31.4 - - - +
37B ARG* 4.0 20.6 - - - +
85B THR* 1.3 72.9 - - - +
87B GLU* 1.3 66.4 + - - +
89B ALA* 3.2 6.7 + - - +
90B HIS* 2.9 46.2 + - + +
115B ASP* 3.6 18.8 - - + +
152B VAL 5.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 2.9 43.2 + - - -
85B THR* 3.3 10.3 - - - +
86B LEU* 1.3 79.5 + - - +
88B GLU* 1.3 65.2 + - - +
90B HIS* 3.2 17.4 + - - +
91B GLU* 3.2 27.7 + - - +
151B ARG* 4.6 7.1 - - - +
152B VAL* 4.6 9.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR 4.8 0.3 - - - +
83B ALA* 3.8 21.9 - - + +
84B SER* 3.0 24.4 + - - -
85B THR* 3.2 21.7 + - - +
87B GLU* 1.3 73.3 - - - +
89B ALA* 1.3 66.8 + - - +
91B GLU* 3.1 19.1 + - + +
92B LYS* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.8 11.0 - - + -
31B TYR* 3.8 36.6 - - + -
81B ILE* 3.6 9.8 - - + +
83B ALA* 3.5 12.0 - - + +
85B THR 3.0 15.1 + - - +
86B LEU* 3.2 11.2 - - - +
88B GLU* 1.3 77.2 - - - +
90B HIS* 1.3 56.2 + - - +
92B LYS 3.3 1.0 + - - -
93B LEU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 3.6 17.9 - + - -
86B LEU* 2.9 32.1 + - + +
87B GLU* 3.3 17.3 - - + +
88B GLU 3.2 0.2 - - - -
89B ALA* 1.3 76.2 - - - +
91B GLU* 1.3 62.7 + - + +
93B LEU* 3.3 1.9 + - - +
94B GLU* 2.9 20.4 + - - +
115B ASP* 2.8 41.2 + - + +
118B ALA* 6.2 0.9 - - + +
119B PRO* 3.2 34.9 - - + +
122B ARG* 4.6 10.0 + - - +
152B VAL* 3.9 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 3.2 15.7 + - - +
88B GLU* 3.1 18.5 + - + +
90B HIS* 1.3 79.1 - - + +
92B LYS* 1.3 58.2 + - + +
94B GLU* 3.3 8.7 + - - +
95B SER* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 3.8 14.4 - - + +
82B THR 2.9 35.5 + - - +
83B ALA* 3.9 12.6 - - + -
88B GLU* 3.1 30.6 + - + +
89B ALA 3.8 2.9 - - - +
91B GLU* 1.3 75.0 - - + +
93B LEU* 1.3 59.8 + - - +
95B SER* 3.7 6.5 - - - -
96B LYS* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.0 18.4 - - + -
29B PHE* 3.9 16.2 - - + -
81B ILE* 3.9 16.5 - - + +
89B ALA 2.9 16.7 + - - +
90B HIS* 3.6 4.0 - - - +
92B LYS* 1.3 74.7 - - - +
94B GLU* 1.3 67.2 + - - +
96B LYS* 3.1 1.8 + - + -
97B VAL* 2.9 37.5 + - + +
109B VAL* 3.9 17.3 - - + -
116B GLN* 3.6 35.9 - - + +
119B PRO* 4.1 5.8 - - + -
120B ASN* 3.4 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B HIS 2.9 17.0 + - - +
91B GLU* 3.6 8.4 - - - +
93B LEU* 1.3 76.5 - - - +
95B SER* 1.3 58.2 + - - +
97B VAL* 4.7 0.7 - - - -
98B PHE* 3.0 28.8 + - - +
119B PRO* 3.4 26.8 - - + +
122B ARG* 3.0 46.2 + - - +
123B ALA* 3.4 9.6 - - - +
126B ARG* 3.1 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU 3.0 17.5 + - - -
92B LYS* 3.7 7.2 - - - -
94B GLU* 1.3 78.7 - - - +
96B LYS* 1.3 59.9 + - - +
98B PHE* 3.4 6.1 + - - +
99B THR* 3.0 35.3 + - - +
126B ARG* 4.7 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 2.6 41.7 + - - -
27B ILE* 3.6 24.7 - - + -
78B ALA* 3.8 20.1 - - - +
81B ILE* 4.1 17.9 - - + -
92B LYS 2.9 17.7 + - - +
93B LEU 3.7 3.6 - - - +
95B SER* 1.3 78.0 - - - +
97B VAL* 1.3 60.8 + - - +
99B THR* 2.6 30.0 + - + +
100B VAL* 3.2 11.0 + - - +
103B ARG* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 4.1 11.2 - - + -
93B LEU* 2.9 23.8 + - + +
94B GLU* 4.5 0.4 - - - -
96B LYS* 1.3 76.0 - - - +
98B PHE* 1.3 64.4 + - - +
100B VAL* 3.2 6.6 + - - +
101B LEU* 3.0 26.7 + - + +
107B PRO* 4.1 6.5 - - + -
109B VAL* 3.8 20.2 - - + -
120B ASN* 3.3 23.6 - - - +
123B ALA* 3.6 20.2 - - + -
268B MET* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU 3.0 19.4 + - - +
95B SER* 3.7 4.9 - - - +
96B LYS 3.3 0.2 - - - -
97B VAL* 1.3 77.6 - - - +
99B THR* 1.3 65.3 + - + +
101B LEU* 3.2 5.0 + - - +
102B ALA* 2.8 44.0 + - + +
123B ALA* 3.6 27.6 - - + -
126B ARG* 3.3 48.5 - - + +
127B ALA* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 3.0 22.8 + - - +
96B LYS* 2.6 28.6 + - - +
98B PHE* 1.3 83.8 - - + +
100B VAL* 1.3 64.3 + - - +
102B ALA* 3.3 13.4 + - - +
103B ARG* 3.4 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.6 22.7 - - - +
25B VAL* 4.3 12.3 - - + -
27B ILE* 4.3 18.8 - - + -
96B LYS* 3.2 17.0 + - - +
97B VAL 3.5 5.8 - - - +
99B THR* 1.3 80.1 + - - +
101B LEU* 1.3 60.2 + - - +
103B ARG* 3.5 13.7 + - - +
105B ALA* 3.1 45.6 + - + +
106B PHE 4.0 2.2 - - - -
107B PRO* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.0 33.0 + - + +
98B PHE* 3.6 6.3 - - - +
100B VAL* 1.3 76.5 - - - +
102B ALA* 1.3 63.3 + - - +
104B GLY* 3.1 13.5 + - - -
105B ALA 4.0 5.2 - - - +
107B PRO* 3.7 15.7 - - + -
123B ALA* 3.8 22.9 - - + +
124B MET* 3.6 31.9 - - - +
127B ALA* 3.9 15.2 - - + +
128B PHE* 4.4 12.4 - - + -
267B MET* 3.6 33.7 - - + +
268B MET* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 2.8 39.0 + - + +
99B THR* 3.6 8.5 - - - +
100B VAL 3.3 0.2 - - - -
101B LEU* 1.3 78.1 - - - +
103B ARG* 1.3 58.4 + - + +
104B GLY 3.3 0.9 + - - -
127B ALA* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 2.7 53.1 + - - +
20B GLU* 3.8 39.4 + - - +
25B VAL* 4.0 9.5 - - - +
96B LYS* 5.6 0.2 - - - +
99B THR* 3.4 25.9 + - - +
100B VAL* 3.6 21.2 - - - +
101B LEU 3.2 0.4 - - - -
102B ALA* 1.3 77.5 - - + +
104B GLY* 1.3 58.7 + - - +
105B ALA* 3.5 10.7 + - + +
----------------------------------------------------------
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