Contacts of the helix formed by residues 83 - 101 (chain A) in PDB entry 3PMM
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 ASP 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 2.8 38.7 + - - -
77A TYR* 3.9 8.3 + - + -
78A TYR* 3.4 9.7 - - - -
81A THR* 3.1 19.9 + - - +
82A GLY* 1.3 72.7 - - - +
84A ILE* 1.3 63.0 + - - +
85A GLU* 2.9 17.2 + - - +
86A MSE 3.2 24.3 + - + +
87A ARG 3.1 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 4.7 3.8 - - + +
82A GLY 3.0 14.1 + - - +
83A ASP* 1.3 71.3 + - - +
85A GLU* 1.3 61.8 + - + +
87A ARG* 3.2 50.2 + - - +
88A ASP* 2.9 36.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
29A ARG* 2.7 37.4 + - - +
83A ASP* 2.9 8.3 + - - +
84A ILE* 1.3 78.8 - - + +
86A MSE 1.3 61.9 + - - +
88A ASP* 3.4 8.9 + - - +
89A ILE* 3.2 28.4 + - - +
92A ARG* 4.8 1.0 + - - -
387A FMT 3.7 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.4 7.2 - - + +
29A ARG* 4.8 7.2 - - - +
32A THR* 3.4 40.4 - - - +
74A ILE* 3.6 35.4 - - + +
77A TYR* 3.8 39.9 - - + -
78A TYR* 4.3 10.1 - - + -
83A ASP* 3.2 29.4 + - + +
85A GLU* 1.3 73.9 - - - +
87A ARG* 1.3 67.4 + - - +
88A ASP 3.2 0.7 + - - -
89A ILE* 3.2 15.3 + - - +
90A ILE* 3.4 8.3 + - - +
368A ILE* 5.1 0.7 - - + -
387A FMT 4.1 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.5 48.1 + - + +
83A ASP 3.1 7.5 + - - +
84A ILE* 3.2 41.7 + - - +
86A MSE 1.3 75.8 - - - +
88A ASP* 1.3 84.6 + - - +
90A ILE* 3.2 11.3 + - - +
91A ASP* 3.1 25.1 + - - +
119A ARG* 3.6 31.9 - - - +
125A ARG* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 2.9 30.6 + - - +
85A GLU* 3.7 7.8 - - - +
86A MSE 3.1 0.4 - - - -
87A ARG* 1.3 101.3 + - - +
89A ILE* 1.3 66.3 + - - +
91A ASP* 4.0 7.6 - - - +
92A ARG* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 4.0 24.9 - - + -
36A VAL* 4.0 15.9 - - + -
60A TRP* 3.8 29.8 + - + +
74A ILE* 4.0 15.7 - - + -
85A GLU 3.2 16.4 + - - +
86A MSE 3.2 14.3 + - - +
88A ASP* 1.3 76.1 - - - +
90A ILE* 1.3 63.3 + - - +
92A ARG* 3.8 22.3 - - - +
93A TRP* 3.1 22.9 + - - +
387A FMT 4.1 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.0 20.2 - - + +
74A ILE* 3.8 16.6 - - + +
75A TYR* 3.5 48.0 - - + +
78A TYR* 5.0 1.8 - - + -
86A MSE 3.4 10.1 + - - +
87A ARG* 3.2 12.9 + - - +
89A ILE* 1.3 77.6 - - - +
91A ASP* 1.3 64.3 + - - +
93A TRP* 3.1 12.1 + - - +
94A PHE* 3.2 39.1 + - + -
115A THR* 3.9 10.1 - - + -
119A ARG* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.1 23.6 + - - +
88A ASP* 3.4 7.9 + - - +
90A ILE* 1.3 78.0 - - - +
92A ARG* 1.3 57.8 + - + +
94A PHE* 3.5 3.6 + - - +
95A ALA* 2.9 29.9 + - - +
119A ARG* 2.9 43.6 + - - +
125A ARG* 3.4 28.5 + - - +
128A TYR* 4.1 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU 4.8 1.0 + - - -
88A ASP* 2.9 45.1 + - + +
89A ILE* 3.8 30.4 - - - +
91A ASP* 1.3 73.8 - - + +
93A TRP* 1.3 60.6 + - - +
95A ALA* 3.7 5.6 - - - +
96A ASP* 2.9 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.0 56.1 + + - +
62A GLY 3.3 18.8 + - - -
63A TRP* 4.1 18.6 - + - -
67A HIS* 3.7 22.3 - - + -
71A LEU* 3.5 25.1 - - + -
89A ILE 3.1 15.5 + - - +
90A ILE 3.1 7.6 + - - +
92A ARG* 1.3 76.8 - - - +
94A PHE* 1.3 96.2 + + - +
96A ASP* 3.3 2.6 + - - +
97A ARG* 2.9 63.0 + - + +
98A PHE* 5.6 0.4 - + - -
112A PRO* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.1 14.8 - - + -
90A ILE* 3.2 40.7 + - + -
91A ASP* 4.0 6.1 - - - +
93A TRP* 1.3 101.7 - + - +
95A ALA* 1.3 64.7 + - - +
97A ARG* 4.6 1.1 - - - -
98A PHE* 2.9 61.4 + + + -
112A PRO* 3.4 30.1 - - + -
113A PHE* 5.4 2.2 - + - -
115A THR* 4.0 4.9 - - + -
116A LEU* 3.7 40.2 - - + -
119A ARG* 5.0 2.2 - - + -
128A TYR* 4.6 11.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
91A ASP 2.9 19.8 + - - +
92A ARG* 3.7 7.9 - - - +
94A PHE* 1.3 76.7 - - - +
96A ASP* 1.3 65.4 + - - +
98A PHE* 3.5 3.1 + - - +
99A ALA* 3.1 25.7 + - - +
128A TYR* 5.8 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 2.9 27.6 + - - +
93A TRP* 3.8 3.5 - - - +
95A ALA* 1.3 80.2 - - - +
97A ARG* 1.3 85.2 + - - +
99A ALA* 3.4 6.8 + - - +
100A GLU* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.8 1.2 + - - -
61A ALA* 3.2 39.5 + - - +
62A GLY 3.7 10.8 - - - -
63A TRP* 4.1 26.4 - - + -
93A TRP* 2.9 72.2 + - + +
94A PHE 3.9 2.0 - - - +
96A ASP* 1.3 96.5 + - - +
98A PHE* 1.3 63.3 + - + +
100A GLU* 2.8 45.1 + - - +
101A GLY 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TRP* 4.1 15.5 - + - -
93A TRP* 5.6 0.4 - + - -
94A PHE* 2.9 55.2 + + + +
95A ALA* 4.2 3.6 - - - +
97A ARG* 1.3 79.2 - - + +
99A ALA* 1.3 65.5 + - - +
101A GLY* 3.3 12.1 + - - +
113A PHE* 4.3 5.6 - + - -
116A LEU* 3.9 21.3 - - + -
127A ALA 5.6 0.2 - - - -
128A TYR* 4.4 12.3 - + - -
131A TRP* 3.4 73.0 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 3.1 19.2 + - - +
96A ASP* 3.7 7.4 - - - +
98A PHE* 1.3 77.1 - - - +
100A GLU* 1.3 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 4.3 7.3 - - - +
63A TRP* 5.9 0.3 - - - -
96A ASP* 3.1 13.0 + - - +
97A ARG* 2.8 52.8 + - - +
99A ALA* 1.3 80.2 - - + +
101A GLY* 1.3 56.9 + - - +
386A FMT 4.0 20.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TRP* 3.9 4.9 - - - -
97A ARG 3.0 16.1 + - - +
98A PHE 3.3 10.6 + - - -
99A ALA 4.6 0.2 - - - -
100A GLU* 1.3 80.7 - - - +
102A ALA* 1.3 66.9 + - - -
103A THR 3.6 1.0 + - - -
131A TRP* 4.4 2.9 - - - -
386A FMT 3.2 14.6 - - - +
----------------------------------------------------------
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