Contacts of the helix formed by residues 83 - 95 (chain A) in PDB entry 4M2O
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 PHE 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.8 17.0 - - + +
13A ILE* 3.7 25.8 - - + -
28A LEU* 3.6 19.3 - - + -
31A TRP* 3.9 13.5 - + + -
32A TYR* 3.6 55.9 - + + -
35A PHE* 3.6 34.1 - + + -
42A GLY 3.6 6.4 + - - +
82A ASP* 1.3 76.4 - - - +
84A LYS* 1.3 57.0 + - - +
86A TYR* 3.3 20.0 + + - +
87A VAL* 2.9 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.8 9.2 - - + +
12A GLU* 3.8 37.9 + - + +
13A ILE* 3.7 27.8 - - + +
16A GLU* 3.1 31.4 + - - +
82A ASP* 3.2 15.1 + - - +
83A PHE* 1.3 80.5 - - - +
85A GLU* 1.3 62.1 + - + +
87A VAL* 3.8 1.9 - - - +
88A ILE* 3.0 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.3 45.0 - - + +
74A ASP* 6.0 0.9 - - - +
80A THR 4.0 3.8 - - - +
81A LEU* 3.4 26.3 - - + +
82A ASP* 2.9 41.3 + - - +
84A LYS* 1.3 78.9 - - + +
86A TYR* 1.3 57.8 + - - +
88A ILE* 4.5 3.6 - - + -
89A ALA* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.0 43.8 + + - -
35A PHE* 3.5 36.4 - + + -
44A ILE* 3.7 22.7 - - + -
49A PHE* 4.7 5.6 - + - -
52A ILE* 3.8 23.3 - - + +
81A LEU* 4.0 17.5 - - + +
82A ASP 3.0 17.9 + - - +
83A PHE* 3.7 15.9 - + - -
85A GLU* 1.3 76.1 - - - +
87A VAL* 1.3 65.0 + - + +
89A ALA* 3.4 3.7 + - - +
90A LEU* 3.1 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.0 24.0 - - + -
17A LEU* 4.5 0.2 - - + -
28A LEU* 4.0 4.7 - - + -
31A TRP* 3.9 23.1 - - + -
83A PHE* 2.9 58.3 + - + +
84A LYS 3.8 3.1 - - - +
86A TYR* 1.3 76.5 - - + +
88A ILE* 1.3 66.6 + - - +
90A LEU* 3.3 2.6 + - - +
91A HIS* 2.7 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.9 4.9 - - + +
16A GLU* 3.5 41.3 - - + +
17A LEU* 3.8 26.9 - - + -
73A PHE* 4.1 17.9 - - + -
84A LYS* 3.0 39.3 + - + +
85A GLU* 3.8 7.0 - - + +
87A VAL* 1.3 74.2 - - - +
89A ALA* 1.3 57.7 + - - +
91A HIS* 3.1 3.9 + - - +
92A MET* 2.8 59.2 + - + +
104A TRP* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.7 27.8 - - + -
53A TYR* 4.2 1.8 - - - -
69A VAL* 3.9 12.3 - - + -
73A PHE* 4.0 15.2 - - + -
81A LEU* 4.6 0.4 - - + -
85A GLU 2.8 17.9 + - - +
86A TYR* 3.6 5.6 - - - +
87A VAL 3.2 0.2 - - - -
88A ILE* 1.3 77.6 - - - +
90A LEU* 1.3 62.2 + - - +
92A MET* 3.2 7.4 + - - +
93A THR* 3.0 28.6 + - - +
104A TRP* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.6 34.1 - - + -
49A PHE* 5.2 3.8 - - + -
52A ILE* 4.7 13.2 - - + -
53A TYR* 3.6 25.4 - - + +
86A TYR* 3.1 41.4 + - + +
87A VAL 3.8 4.3 - - - +
88A ILE 3.3 0.2 - - - -
89A ALA* 1.3 75.4 - - - +
91A HIS* 1.3 64.3 + - - +
93A THR* 3.8 3.8 - - - +
94A SER* 3.0 34.7 + - - +
95A ALA* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.5 28.3 - - + +
20A ASN* 3.4 27.4 - - + +
21A THR* 3.9 1.1 + - - -
22A LYS* 3.3 32.2 + - + +
23A PHE* 3.6 24.8 - + - -
28A LEU* 5.2 0.2 - - + -
31A TRP* 4.5 2.5 - + - -
87A VAL* 2.7 48.6 + - + +
88A ILE 3.1 7.8 + - - +
90A LEU* 1.3 78.9 - - - +
92A MET* 1.3 60.9 + - + +
95A ALA* 2.9 43.1 + - + +
101A LYS* 3.3 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 6.5 0.4 - - + -
17A LEU* 4.5 12.1 - - + -
20A ASN* 4.6 13.5 - - - +
88A ILE* 2.8 37.8 + - + +
89A ALA 3.2 5.4 + - - +
91A HIS* 1.3 77.5 - - - +
93A THR* 1.3 58.4 + - - +
100A GLN 5.4 0.2 - - - +
101A LYS* 2.8 51.3 + - + +
104A TRP* 3.5 65.1 - - + +
188A PHE* 3.4 15.4 - - - -
189A GLU* 3.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 2.8 34.8 + - - +
57A PHE* 5.9 0.4 - - - -
65A TYR* 3.2 37.0 - - + +
69A VAL* 3.8 19.1 - - + -
89A ALA 3.0 8.5 + - - +
90A LEU 3.3 5.7 + - - -
92A MET* 1.3 78.8 - - + +
94A SER* 1.3 76.8 + - - +
104A TRP* 5.0 2.0 - - + -
188A PHE* 5.0 0.9 - - - -
189A GLU* 3.3 22.4 - - - +
190A PRO* 3.6 11.9 - - - +
191A GLN 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 4.8 1.4 + - - -
57A PHE* 4.8 12.3 - - - -
90A LEU* 3.0 19.2 + - - +
91A HIS 3.3 0.6 + - - -
92A MET 3.3 0.2 - - - -
93A THR* 1.3 94.9 + - - +
95A ALA* 1.3 62.7 + - - +
101A LYS* 4.9 0.2 - - - -
189A GLU* 4.9 2.2 - - - -
192A LYS* 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 5.3 1.6 - - - +
22A LYS* 3.3 34.3 - - + +
90A LEU 5.0 0.2 - - - +
91A HIS* 2.9 28.1 + - + +
94A SER* 1.3 76.2 - - - +
96A GLY* 1.3 60.8 + - - +
101A LYS* 2.6 34.8 + - - +
192A LYS* 5.6 0.9 - - - -
----------------------------------------------------------
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