Contacts of the helix formed by residues 82 - 104 (chain A) in PDB entry 3MTS
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 CYS 82 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.7 42.8 - - + +
48A LEU* 4.7 1.8 - - - -
80A LEU* 3.6 13.2 - - - -
81A LYS* 1.3 77.3 - - + +
83A VAL* 1.3 58.3 + - - +
84A ARG 3.4 2.0 - - - -
85A ILE* 3.4 23.2 + - + -
86A LEU* 3.0 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.0 22.9 - - - +
81A LYS* 2.8 21.2 + - - +
82A CYS* 1.3 72.6 - - - +
84A ARG* 1.3 66.5 - - + +
86A LEU* 3.3 7.5 + - - +
87A LYS* 3.0 32.3 + - - +
68C PRO* 5.7 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A CYS 3.4 0.8 - - - -
83A VAL* 1.3 84.4 - - + +
85A ILE* 1.3 62.7 + - + +
87A LYS* 3.3 7.8 + - - +
88A GLN* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.5 10.5 - - + +
46A GLU 4.9 11.7 - - - +
47A TYR* 4.6 4.5 - - + -
48A LEU* 3.8 33.7 - - + +
82A CYS* 3.4 24.6 + - + +
83A VAL 3.4 0.2 - - - -
84A ARG* 1.3 78.0 - - + +
86A LEU* 1.3 60.4 + - - +
88A GLN* 3.4 8.0 + - + +
89A PHE* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.6 16.8 - - + -
60A TYR* 3.3 49.6 - - + +
77A ARG* 3.7 37.9 - - - +
80A LEU* 4.5 7.0 - - + -
82A CYS* 3.0 36.9 + - - +
83A VAL* 3.6 7.2 - - - +
84A ARG 3.3 0.2 - - - -
85A ILE* 1.3 77.2 - - - +
87A LYS* 1.3 51.7 + - - +
89A PHE* 3.3 0.9 + - - +
90A HIS* 2.8 46.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.0 19.0 + - - +
84A ARG* 3.5 7.2 - - - +
86A LEU* 1.3 75.9 - - - +
88A GLN* 1.3 58.1 + - - +
90A HIS* 3.1 6.8 + - + +
91A LYS* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 3.0 16.8 + - - +
85A ILE* 3.9 11.2 - - + +
87A LYS* 1.3 75.9 - - - +
89A PHE* 1.3 57.4 + - - +
91A LYS* 3.4 6.7 + - - +
92A ASP* 2.8 71.6 + - - +
95A ARG* 4.6 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 33.2 - - + -
49A CYS 4.2 2.2 - - - -
50A ASP* 3.7 28.7 - - - -
51A TYR* 3.6 34.1 - + + -
60A TYR* 3.9 22.4 - + - -
85A ILE* 2.9 18.0 + - + +
86A LEU 3.6 2.5 - - - +
88A GLN* 1.3 77.3 - - - +
90A HIS* 1.3 67.8 + + - +
92A ASP* 3.3 8.5 + - + +
93A LEU* 2.9 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 4.0 32.8 - + - -
58A GLU* 5.1 2.1 + - - -
60A TYR* 2.4 34.6 + + - -
86A LEU* 2.8 34.8 + - + +
87A LYS* 3.8 5.6 - - + +
89A PHE* 1.3 79.9 - + - +
91A LYS* 1.3 56.1 + - + +
93A LEU* 3.3 9.9 + - + +
94A GLU* 2.7 36.8 + - - +
94B GLU* 4.0 20.3 + - - +
98B LEU* 4.6 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 2.9 39.1 + - + +
88A GLN* 3.8 10.8 - - - +
90A HIS* 1.3 76.1 - - + +
92A ASP* 1.3 63.7 + - - +
94A GLU* 2.6 36.1 + - - +
95A ARG* 2.9 40.7 + - - +
90B HIS* 6.3 0.2 - - - +
94B GLU* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 2.8 51.1 + - - +
89A PHE* 3.5 7.9 - - + +
91A LYS* 1.3 78.3 - - - +
93A LEU* 1.3 62.9 + - - +
95A ARG* 2.6 46.1 + - - +
96A GLU* 3.2 12.8 + - - +
99A ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 4.2 17.7 - - + -
89A PHE* 2.9 38.2 + - + +
90A HIS* 3.8 8.7 - - - +
92A ASP* 1.3 72.1 - - - +
94A GLU* 1.3 68.0 + - - +
96A GLU* 3.0 12.8 + - + +
97A LEU* 2.9 41.7 + - + +
98B LEU* 3.6 25.8 - - + -
101B HIS* 4.2 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS 2.7 21.9 + - - +
91A LYS* 2.6 41.3 + - - +
93A LEU* 1.3 72.7 - - - +
95A ARG* 1.3 57.2 + - - +
97A LEU* 3.3 9.4 + - - +
98A LEU* 2.9 46.7 + - + +
90B HIS* 3.9 34.3 + - - +
94B GLU* 4.1 35.9 + - + +
97B LEU* 6.3 0.7 - - + -
98B LEU* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 4.6 3.2 - - - +
91A LYS* 2.9 29.8 + - + +
92A ASP* 2.6 45.5 + - - +
93A LEU 3.2 0.2 - - - -
94A GLU* 1.3 76.9 - - + +
96A GLU* 1.3 57.5 + - - +
98A LEU* 3.3 10.8 + - + +
99A ARG* 2.9 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP 3.2 7.8 + - - +
93A LEU* 3.0 17.5 + - + +
95A ARG* 1.3 76.2 - - - +
97A LEU* 1.3 60.7 + - + +
99A ARG* 3.3 32.2 + - - +
100A ARG* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 2.9 34.2 + - + +
94A GLU* 3.9 7.0 - - - +
96A GLU* 1.3 72.1 - - + +
98A LEU* 1.3 60.7 + - - +
100A ARG* 3.3 10.2 + - + +
101A HIS* 2.8 28.1 + - - +
94B GLU* 5.3 1.6 - - + +
97B LEU* 3.8 34.6 - - + +
98B LEU* 3.7 33.4 - - + -
101B HIS* 3.8 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 2.9 43.4 + - + +
95A ARG* 3.6 11.0 - - + +
97A LEU* 1.3 72.3 - - - +
99A ARG* 1.3 66.5 + - - +
101A HIS* 2.9 17.9 + - + +
102A HIS* 3.0 27.6 + - + -
51B TYR* 4.1 28.3 - - + +
90B HIS* 4.6 8.1 - - + +
93B LEU* 3.9 25.4 - - + -
94B GLU* 6.0 0.9 - - - +
97B LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 2.9 34.1 + - + +
96A GLU* 3.3 34.7 + - - +
98A LEU* 1.3 73.1 - - - +
100A ARG* 1.3 59.3 + - - +
102A HIS* 3.4 9.7 + - - +
103A ARG* 3.3 19.2 + - - +
53B LYS* 6.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU 3.0 13.2 + - - +
97A LEU* 3.5 15.9 - - + +
99A ARG* 1.3 72.7 - - - +
101A HIS* 1.3 63.2 + - - +
103A ARG* 3.5 20.3 - - - +
104A SER* 3.6 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 2.8 17.4 + - - +
98A LEU* 2.9 21.6 + - + +
100A ARG* 1.3 71.9 - - - +
102A HIS* 1.3 78.8 + + - +
104A SER* 3.4 21.8 + - - -
50B ASP* 5.1 5.0 + - - -
51B TYR* 4.7 12.0 + + - +
93B LEU* 4.0 25.7 - - + +
97B LEU* 3.9 29.3 - - + +
100B ARG* 4.0 11.9 + - - +
99C ARG* 4.4 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.0 31.2 + - + -
99A ARG* 3.6 10.4 + - - +
100A ARG 3.3 0.2 - - - -
101A HIS* 1.3 82.3 - + - +
103A ARG* 1.3 65.8 + - - +
104A SER 3.1 6.8 + - - -
51B TYR* 3.4 38.4 + + - -
52B LYS* 3.6 11.0 - - + -
53B LYS* 3.1 52.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG 3.3 9.8 + - - +
100A ARG* 3.5 15.7 - - - +
102A HIS* 1.3 79.6 - - - +
104A SER* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG 3.6 11.3 + - - -
101A HIS* 3.4 14.9 + - - -
102A HIS 3.1 9.3 - - - -
103A ARG* 1.3 81.0 - - - +
----------------------------------------------------------
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