Contacts of the helix formed by residues 81 - 100 (chain B) in PDB entry 5AIS
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 81 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN* 1.3 82.5 - - - +
82B GLU* 1.3 64.9 + - - +
83B MET* 3.6 7.7 + - - +
84B GLU* 3.1 29.6 + - - +
85B GLN* 3.0 30.3 + - - +
26C ASP* 3.5 23.3 - - - +
27C ILE 4.3 0.7 - - - -
28C GLN* 3.7 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 3.5 31.7 + - + +
73A LYS* 4.1 30.6 - - + +
74A ASN* 3.4 20.1 + - - -
81B THR* 1.3 73.7 - - - +
83B MET* 1.3 61.8 + - - +
85B GLN* 3.4 14.1 + - - +
86B CYS 3.2 15.4 + - - -
26C ASP* 3.1 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.3 22.0 - - + -
59A LEU* 3.5 39.9 - - + -
61A LEU* 4.4 15.9 - - + -
70A TYR* 3.9 29.5 - - + +
81B THR* 3.2 7.6 + - - +
82B GLU* 1.3 76.9 - - - +
84B GLU* 1.3 64.6 + - + +
86B CYS* 3.1 5.8 + - - +
87B HIS* 3.0 47.2 + - + +
26C ASP* 4.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY* 3.9 3.6 - - - -
80B ASN* 3.1 30.9 + - - +
81B THR* 3.1 28.4 + - - +
83B MET* 1.3 76.1 - - + +
85B GLN* 1.3 57.6 + - - +
87B HIS* 3.2 9.1 + - + +
88B VAL* 2.8 32.9 + - - +
142B ILE* 3.5 19.5 - - + +
143B GLY* 3.2 23.2 - - - +
147B THR* 5.4 1.9 - - - +
28C GLN* 2.7 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 4.1 30.1 + - - +
73B LYS* 6.0 4.8 - - - +
78B ALA* 4.7 9.0 - - + +
79B GLY* 3.6 32.7 - - - +
80B ASN 5.5 0.2 - - - -
81B THR* 3.0 19.9 + - - +
82B GLU* 3.5 14.6 + - - +
83B MET 3.3 0.2 - - - -
84B GLU* 1.3 75.4 - - - +
86B CYS* 1.3 62.5 + - - +
88B VAL* 3.5 5.5 + - - +
89B ASP* 3.1 31.4 + - - +
193C ARG* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.0 32.8 - - + -
62A HIS 5.0 1.6 - - - -
66A ALA* 3.6 30.4 - - - +
67A ILE* 4.2 4.0 - - - -
70A TYR* 3.8 23.3 - - + +
82B GLU 3.2 8.9 + - - +
83B MET* 3.1 11.6 + - - +
85B GLN* 1.3 77.3 - - - +
87B HIS* 1.3 59.5 + - - +
89B ASP* 3.3 7.9 + - - +
90B ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 6.0 1.5 - - + +
60A THR 3.8 11.7 - - - -
61A LEU* 3.5 25.5 - - + +
62A HIS* 5.5 6.0 + + - -
83B MET* 3.0 45.0 + - + +
84B GLU* 3.2 12.1 + - + +
86B CYS* 1.3 72.3 - - - +
88B VAL* 1.3 66.1 + - - +
90B ALA* 3.7 6.1 - - - +
91B ILE* 3.0 30.1 + - - +
134B TYR* 3.6 25.0 + + - +
142B ILE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY 4.4 10.5 - - - +
84B GLU 2.8 22.1 + - - +
85B GLN* 3.6 7.0 - - - +
86B CYS 3.3 0.2 - - - -
87B HIS* 1.3 78.8 - - - +
89B ASP* 1.3 65.0 + - - +
91B ILE* 4.0 1.6 - - - +
92B VAL* 3.1 25.1 + - + +
142B ILE* 3.8 27.1 - - + -
147B THR* 3.9 20.4 - - + +
148B TRP* 3.4 40.4 - - + +
149B ALA* 4.1 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.7 16.0 - - + +
69A ARG* 3.1 31.7 + - - +
69B ARG* 3.1 33.9 + - - +
85B GLN* 3.1 19.0 + - - +
86B CYS* 3.7 6.5 - - - +
88B VAL* 1.3 81.2 - - - +
90B ALA* 1.3 58.9 + - - +
92B VAL* 3.6 4.9 + - - +
93B ASP* 3.0 34.8 + - - +
148B TRP* 4.0 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 3.5 46.0 - - + +
63A GLN* 3.4 14.5 - - + +
66A ALA* 3.7 1.3 - - + +
86B CYS* 2.9 17.9 + - - +
87B HIS* 3.7 9.0 - - - +
88B VAL 3.2 0.2 - - - -
89B ASP* 1.3 75.6 - - - +
91B ILE* 1.3 59.4 + - - +
93B ASP 3.5 0.2 + - - -
94B THR* 3.0 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.7 26.5 - - + -
62A HIS* 4.6 3.1 - - - +
87B HIS 3.0 21.2 + - - +
88B VAL 4.0 2.7 - - - +
90B ALA* 1.3 73.8 - - - +
92B VAL* 1.3 66.5 + - - +
94B THR* 3.3 4.8 + - - -
95B LEU* 3.0 40.2 + - + +
131B LEU* 5.2 8.3 - - + -
134B TYR* 3.4 44.6 - - + -
141B LEU* 4.2 23.1 - - + -
142B ILE* 4.4 9.2 - - + -
149B ALA* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.5 37.7 - - + -
69B ARG* 5.7 0.9 - - - +
88B VAL 3.1 19.4 + - - +
89B ASP* 3.9 4.3 - - - +
91B ILE* 1.3 76.1 - - + +
93B ASP* 1.3 53.6 + - - +
95B LEU* 3.3 2.0 + - - -
96B ASP* 2.8 32.9 + - - +
148B TRP* 3.8 28.9 - - + -
149B ALA* 3.9 26.2 - - - +
152B TYR* 3.6 22.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN* 3.5 28.3 - - + +
65A LEU* 4.4 22.3 - - - +
66A ALA* 4.5 6.8 + - - +
69A ARG* 5.4 3.1 + - - -
93A ASP* 5.3 5.5 - - - +
1201A GSH 5.5 0.2 - - - +
65B LEU* 3.7 19.2 - - - +
69B ARG* 4.7 8.9 + - - -
89B ASP* 3.0 20.7 + - - +
90B ALA 3.8 0.2 - - - +
92B VAL* 1.3 74.4 - - - +
94B THR* 1.3 57.3 + - - +
96B ASP* 3.7 4.2 - - - +
97B ASP* 2.7 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.9 24.5 - - + +
62A HIS* 3.4 16.9 + - - -
63A GLN* 3.2 16.0 + - - +
90B ALA 3.0 18.7 + - - -
91B ILE* 3.5 8.1 - - - -
93B ASP* 1.3 75.5 - - - +
95B LEU* 1.3 64.4 + - + +
97B ASP* 3.6 4.9 + - - +
98B PHE* 3.4 19.9 + - - +
127B LEU* 3.8 25.5 - - + +
131B LEU* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.0 35.2 + - + +
92B VAL 3.6 5.4 - - - +
94B THR* 1.3 76.4 - - - +
96B ASP* 1.3 62.3 + - - +
98B PHE* 3.2 7.0 + - - +
99B MET* 3.1 27.6 + - + +
127B LEU* 4.4 12.1 - - + -
131B LEU* 3.8 31.4 - - + -
141B LEU* 5.4 0.2 - - + -
149B ALA 4.5 2.2 - - - +
152B TYR* 3.8 19.3 - - + +
153B TRP* 3.9 44.4 - - + +
156B CYS* 4.1 11.7 - - + -
160B LEU* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.5 1.6 - - - +
14B ARG* 4.9 3.3 + - - +
64B SER* 5.0 1.2 + - - -
65B LEU* 3.6 26.3 - - + +
92B VAL 2.8 20.4 + - - +
93B ASP* 3.7 5.2 - - - +
95B LEU* 1.3 74.3 - - - +
97B ASP* 1.3 61.7 + - - +
99B MET* 3.9 3.0 - - - +
100B SER* 2.8 39.6 + - - -
152B TYR* 2.6 30.1 + - - +
1200B CWC 3.3 13.0 - - - -
1201B MG 3.9 13.2 - - - -
1202B GSH 5.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 5.2 12.3 + - - +
63A GLN* 3.1 12.6 + - - -
96A ASP* 5.5 1.0 - - - +
1201A GSH 2.7 35.9 + - - +
93B ASP* 2.7 25.8 + - - +
94B THR* 3.6 7.1 - - - +
96B ASP* 1.3 74.4 - - - +
98B PHE* 1.3 60.9 + - - +
100B SER* 3.5 5.9 + - - -
101B CYS* 3.4 24.1 + - - -
1201B MG 3.9 16.6 - - - -
----------------------------------------------------------
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 THR 3.4 5.2 + - - +
95B LEU 3.2 8.5 + - - +
97B ASP* 1.3 76.6 - - - +
99B MET* 1.3 69.4 + - - +
101B CYS* 3.0 25.3 + - - +
102B PHE* 3.6 29.9 - + - -
119B LEU* 3.7 19.7 - - + -
123B ASN* 3.6 28.9 - - + -
124B ALA* 3.6 33.7 - - + -
127B LEU* 3.6 32.5 - - + -
160B LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.1 17.8 + - + +
96B ASP 4.0 0.2 - - - +
98B PHE* 1.3 79.6 - - + +
100B SER* 1.3 60.1 + - - +
101B CYS 3.4 0.5 + - - -
102B PHE* 3.4 11.1 + - + -
104B TRP* 2.9 50.1 + - + -
156B CYS* 3.6 37.2 - - + +
159B THR* 4.1 20.4 - - + -
160B LEU* 3.9 32.8 - - + -
1200B CWC 3.3 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 5.8 0.2 + - - -
14B ARG* 3.1 23.6 + - - +
96B ASP* 2.8 32.3 + - - -
97B ASP* 3.8 7.6 - - - -
98B PHE 3.1 0.2 - - - -
99B MET* 1.3 76.2 - - - +
101B CYS* 1.3 62.9 + - - +
102B PHE 3.3 6.6 + - - +
104B TRP* 4.9 1.5 - - - +
1200B CWC 3.8 8.1 - - - -
1202B GSH 5.8 0.3 + - - -
----------------------------------------------------------
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