Contacts of the helix formed by residues 70 - 88 (chain A) in PDB entry 1MDU
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 SER 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 4.5 0.2 + - - -
68A GLU 3.8 1.0 + - - -
69A CYS* 1.3 73.7 - - - +
71A GLN* 1.3 57.8 + - - +
72A ASP* 2.3 26.5 + - - -
73A GLU* 2.7 41.1 + - - +
74A SER* 3.2 10.5 + - - -
123A SER* 3.4 20.5 + - - -
125A PHE* 5.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS 4.1 0.6 + - - -
70A SER* 1.3 73.1 - - - +
72A ASP* 1.3 58.3 + - - +
74A SER* 3.0 10.6 + - - -
75A GLY* 2.8 28.4 + - - -
125A PHE* 4.6 8.4 - - + -
146B ALA* 2.8 42.9 + - - +
334B PRO* 5.8 5.7 - - - +
336B GLU* 4.9 7.8 - - - +
340B SER* 5.7 1.0 + - - +
343B ILE* 3.6 38.0 - - + +
347B ILE* 3.9 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 5.4 0.7 - - - +
24A LYS* 5.5 0.9 - - - -
25A PHE* 4.0 20.5 + - + -
70A SER* 2.3 32.0 + - - -
71A GLN* 1.3 80.3 - - - +
73A GLU* 1.3 72.8 + - - +
76A ALA* 3.0 28.4 + - - +
123A SER* 3.1 12.9 + - - -
124A GLY* 3.1 20.1 + - - -
125A PHE* 3.4 34.6 - - + -
347B ILE* 3.9 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.9 27.0 - - + +
24A LYS 5.7 3.8 + - - +
41A GLY 3.1 6.2 - - - +
42A ASP* 3.4 10.3 - - - +
43A ALA* 3.6 16.8 - - + +
69A CYS* 3.4 4.1 - - + +
70A SER* 2.7 37.2 + - - +
72A ASP* 1.3 85.3 - - - +
74A SER* 1.3 60.9 + - - +
75A GLY 3.1 1.3 - - - -
76A ALA* 3.8 0.9 - - - +
77A ALA* 2.9 30.7 + - - +
121A VAL* 3.3 9.4 - - - +
122A ALA 4.3 5.2 - - - +
123A SER* 5.0 1.3 - - - -
402A CA 2.4 31.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA* 4.2 0.8 - - - +
65A LEU* 3.7 31.8 - - - +
69A CYS* 3.8 13.4 - - - -
70A SER 3.2 2.7 + - - -
71A GLN* 3.0 26.7 + - - +
73A GLU* 1.3 77.4 - - - +
75A GLY* 1.3 60.3 + - - +
77A ALA* 3.6 1.9 + - - +
78A ALA* 3.1 23.4 + - - +
146B ALA 4.9 1.6 + - - -
147B SER 5.4 0.6 - - - -
148B GLY* 3.6 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 2.8 18.3 + - - -
72A ASP 4.0 0.7 - - - -
74A SER* 1.3 77.7 + - - +
76A ALA* 1.3 55.9 + - - +
78A ALA* 3.3 4.9 + - - +
79A ILE* 2.9 32.7 + - - +
145B TYR 3.3 23.0 - - - +
146B ALA 5.1 0.2 - - - -
148B GLY* 4.7 0.6 - - - +
347B ILE* 4.1 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.8 22.2 - - + -
25A PHE* 4.9 4.0 - - + -
72A ASP 3.0 19.7 + - - +
75A GLY* 1.3 73.7 - - - +
77A ALA* 1.3 56.1 + - - +
79A ILE* 3.1 3.2 + - - +
80A PHE* 2.7 46.4 + - + -
347B ILE* 3.9 3.9 - - + +
351B LEU* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.8 18.8 - - + +
43A ALA* 4.0 12.6 - - + -
44A TYR 4.4 2.7 - - - +
45A VAL* 3.8 12.0 - - + +
63A TYR* 4.3 11.9 - - + -
65A LEU* 4.2 10.1 - - + -
73A GLU 2.9 18.4 + - - +
74A SER 3.8 4.3 - - - +
76A ALA* 1.3 76.3 - - - +
78A ALA* 1.3 61.7 + - - +
80A PHE* 3.5 0.4 + - - -
81A THR* 2.9 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.2 9.8 - - + -
74A SER 3.1 15.1 + - - +
75A GLY 3.6 4.5 - - - +
76A ALA 3.2 0.2 - - - -
77A ALA* 1.3 77.5 - - - +
79A ILE* 1.3 64.4 + - - +
81A THR* 3.4 1.5 + - - -
82A VAL* 3.3 14.1 + - - +
145B TYR* 4.6 7.2 - - + +
148B GLY* 4.0 3.4 - - - -
149B ARG 3.8 25.8 - - - +
150B THR* 3.3 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 2.9 20.9 + - - +
76A ALA 3.1 0.4 + - - +
78A ALA* 1.3 76.2 - - - +
80A PHE* 1.3 62.0 + - - +
82A VAL* 3.2 9.4 + - + +
83A GLN* 3.1 39.4 + - + +
145B TYR* 3.7 38.8 - - + -
344B GLY 4.7 0.9 - - - +
347B ILE* 4.0 16.2 - - + -
348B LEU* 3.8 44.6 - - + +
351B LEU* 3.3 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.5 5.6 - + - -
22A VAL* 4.3 5.4 - - + -
25A PHE 3.7 20.4 - - - -
26A ASP* 3.9 25.6 - - - -
27A LEU* 3.6 35.2 - - + -
45A VAL* 4.1 11.7 - - + -
76A ALA* 2.7 45.4 + - + +
77A ALA 3.8 3.6 - - - +
79A ILE* 1.3 73.9 - - - +
81A THR* 1.3 56.3 + - - +
83A GLN* 3.3 14.8 + - - +
84A LEU* 2.8 34.1 + - - +
351B LEU* 4.0 11.2 - - + -
352B SER* 4.5 2.2 - - - -
353B THR* 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.1 12.4 - - - +
61A LEU* 3.4 22.4 - - + +
63A TYR* 3.4 35.3 + - + +
77A ALA 2.9 22.0 + - - -
78A ALA 3.6 5.2 - - - -
79A ILE 3.3 0.2 - - - -
80A PHE* 1.3 75.3 - - - +
82A VAL* 1.3 59.0 + - - +
84A LEU* 4.5 3.6 - - - -
85A ASP* 2.9 28.2 + - - +
94A GLN* 3.5 30.7 - - + +
150B THR* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA 3.3 12.0 + - - +
79A ILE* 3.2 10.9 + - + +
81A THR* 1.3 77.8 - - - +
83A GLN* 1.3 54.1 + - + +
85A ASP* 3.1 4.9 + - - +
86A ASP* 2.8 51.5 + - - +
94A GLN* 4.0 9.0 - - - +
145B TYR* 4.3 15.0 - - + +
150B THR* 3.7 16.6 - - + -
169B GLU 3.9 4.5 - - - +
170B GLY* 3.4 30.3 - - - +
171B TYR* 4.1 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 3.9 22.0 + - + +
8A PHE* 3.7 13.9 - - + -
79A ILE* 3.1 31.2 + - + +
80A PHE* 3.3 23.6 - - - +
82A VAL* 1.3 77.3 - - + +
84A LEU* 1.3 59.4 + - - +
86A ASP* 3.2 10.7 + - - +
87A TYR* 2.8 29.5 + - - +
348B LEU* 5.1 3.2 - - - +
351B LEU* 4.5 2.4 - - - +
353B THR* 2.7 35.4 + - - +
354B PHE* 5.0 2.2 - - - +
357B MET* 4.1 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.7 37.9 - - + +
11A ALA* 4.1 22.4 - - + -
20A TRP* 3.8 26.2 - - + -
27A LEU* 4.6 7.9 - - + -
45A VAL* 3.9 13.2 - - + -
47A LEU* 5.2 3.6 - - + -
61A LEU* 3.8 28.7 - - + -
80A PHE 2.8 19.6 + - - +
81A THR 3.8 3.8 - - - +
83A GLN* 1.3 72.6 - - - +
85A ASP* 1.3 62.6 + - - +
87A TYR* 3.3 5.9 + - + +
88A LEU* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.7 10.5 - - + +
81A THR 2.9 15.4 + - - +
82A VAL 3.3 8.7 - - - +
84A LEU* 1.3 78.1 - - - +
86A ASP* 1.3 56.3 + - - +
88A LEU* 3.0 8.5 + - - -
90A GLY* 2.6 54.8 + - - -
92A ALA* 3.0 20.6 + - - +
94A GLN* 3.0 25.7 + - - +
403A CA 2.4 22.6 - - - -
169B GLU* 3.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL 5.9 1.6 - - - +
82A VAL* 2.8 27.1 + - - +
83A GLN* 3.2 11.1 + - - +
85A ASP* 1.3 77.8 - - - +
87A TYR* 1.3 58.3 + - - +
89A ASN* 2.9 22.2 + - - -
90A GLY* 4.0 7.3 - - - +
169B GLU 5.4 0.3 - - - +
171B TYR* 2.5 41.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL 4.3 5.8 - - - +
3A VAL* 3.7 51.4 - - + +
8A PHE* 3.2 45.4 + + + -
9A LEU* 3.7 19.3 + - - +
11A ALA* 4.8 4.5 - - + -
83A GLN 2.8 17.2 + - - +
84A LEU* 3.5 7.9 - - + +
86A ASP* 1.3 76.2 - - - +
88A LEU* 1.3 76.2 + - + +
89A ASN* 3.0 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.3 16.4 - - + +
47A LEU* 4.3 17.5 - - + -
59A TYR* 3.7 58.3 - - + +
61A LEU* 5.1 1.8 - - + -
84A LEU* 3.0 23.8 + - + +
85A ASP* 3.0 7.3 + - - +
87A TYR* 1.3 93.5 - - + +
89A ASN* 1.3 73.2 + - - +
90A GLY 3.0 2.8 + - - -
91A ARG* 3.1 24.8 + - - +
92A ALA* 4.5 9.2 - - + +
----------------------------------------------------------
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