Contacts of the helix formed by residues 85 - 104 (chain R) in PDB entry 3SDI
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 ALA 85 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R MET* 4.1 20.9 - - - -
82R THR 3.0 14.9 + - - +
84R ASP* 1.3 78.0 - - - +
86R ARG* 1.3 66.8 + - - +
87R SER 3.3 1.1 - - - -
88R MET* 3.1 8.6 + - - +
89R ILE* 2.9 31.0 + - + +
134R VAL* 4.1 21.5 - - + +
136R LEU* 4.5 13.0 - - + -
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Residues in contact with ARG 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Q ARG* 5.4 11.2 - - + +
118Q GLY* 6.0 7.4 - - - -
121Q GLN* 5.9 2.2 - - + +
155Q GLY 5.9 2.0 - - - +
157Q TYR* 4.7 24.3 - - + -
65R GLU* 3.8 29.7 + - - +
68R VAL* 4.6 10.7 - - - +
78R MET* 4.1 18.9 - - - +
82R THR* 3.7 28.1 + - - -
83R ALA* 3.6 18.0 + - - +
84R ASP 3.4 0.8 - - - -
85R ALA* 1.3 76.0 - - - +
87R SER* 1.3 57.5 + - - +
89R ILE* 3.3 11.4 + - - +
90R GLU* 2.9 30.4 + - - +
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Residues in contact with SER 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121Q GLN* 5.7 6.3 - - - -
125Q GLN* 4.9 2.9 + - - -
83R ALA 5.0 0.2 + - - -
84R ASP 4.0 3.7 + - - -
85R ALA 3.3 0.4 - - - -
86R ARG* 1.3 78.6 - - - +
88R MET* 1.3 60.1 + - - +
90R GLU* 3.9 7.8 - - - +
91R HIS* 3.1 27.5 + - - +
119R LEU* 3.8 6.2 - - - +
132R PHE* 3.8 24.8 - - - -
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Residues in contact with MET 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R ASP 3.8 10.3 - - - +
85R ALA* 3.1 7.1 + - - +
87R SER* 1.3 76.5 + - - +
89R ILE* 1.3 55.8 + - - +
91R HIS* 3.3 2.8 + - - +
92R ALA* 2.8 35.3 + - - +
116R VAL* 3.6 35.5 - - + +
119R LEU* 4.1 8.5 - - + -
120R ALA* 4.8 5.8 - - + -
132R PHE* 3.8 42.0 - - + -
134R VAL* 3.8 32.3 - - - +
136R LEU* 3.6 26.5 - - + -
151R ALA* 5.5 5.8 - - + +
152R GLU 5.9 2.5 - - - +
153R PRO* 6.0 1.8 - - + -
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Residues in contact with ILE 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R VAL* 3.4 22.7 - - + -
69R GLU 4.6 0.9 - - - +
70R ILE* 4.9 7.2 - - + -
76R CYS* 3.4 33.9 - - - -
78R MET* 4.7 4.0 - - + -
85R ALA* 2.9 26.4 + - + +
86R ARG* 3.7 15.5 - - - +
88R MET* 1.3 75.2 - - - +
90R GLU* 1.3 53.3 + - - +
92R ALA* 3.2 6.2 + - + +
93R ARG* 2.8 68.1 + - + +
136R LEU* 4.6 12.8 - - + -
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Residues in contact with GLU 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ARG 2.9 17.8 + - - +
87R SER* 3.9 8.1 - - - +
89R ILE* 1.3 74.5 - - - +
91R HIS* 1.3 66.3 + - - +
93R ARG* 3.2 10.1 + - - +
94R THR* 3.0 43.2 + - - +
69Y ARG* 2.5 49.5 + - - -
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Residues in contact with HIS 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R SER 3.1 18.2 + - - +
88R MET 3.5 3.8 - - - +
90R GLU* 1.3 79.6 - - - +
92R ALA* 1.3 61.4 + - - +
94R THR* 3.8 5.9 - - - -
95R ALA* 3.0 27.2 + - + +
115R SER* 2.9 44.7 + - - -
116R VAL* 4.3 7.4 - - + -
118R ASP* 6.2 0.4 - - + -
119R LEU* 3.7 29.9 - - + +
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Residues in contact with ALA 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ILE* 3.8 25.4 - - + -
88R MET 2.8 21.6 + - - +
89R ILE* 3.5 7.0 - - + +
91R HIS* 1.3 76.1 - - - +
93R ARG* 1.3 57.2 + - - +
95R ALA 3.4 0.5 + - - -
96R ALA* 3.0 25.8 + - - +
112R LEU* 3.2 22.3 - - + +
116R VAL* 3.7 22.0 - - + -
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Residues in contact with ARG 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R GLU* 5.3 2.6 + - - -
68R VAL* 4.0 12.9 - - - +
69R GLU* 2.8 29.1 + - - +
70R ILE* 3.5 27.5 - - - +
89R ILE* 2.8 40.2 + - - +
90R GLU* 3.6 12.8 + - - +
92R ALA* 1.3 74.3 - - - +
94R THR* 1.3 59.7 + - - +
96R ALA* 3.2 2.8 + - - +
97R VAL* 2.9 34.3 + - - +
65Y LEU* 4.1 15.0 - - + -
68Y LEU* 3.3 44.2 + - + +
69Y ARG* 4.1 17.2 + - - +
71Y LYS* 5.9 3.0 - - - +
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Residues in contact with THR 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R GLU* 3.0 34.7 + - - +
91R HIS* 3.8 6.1 - - - -
93R ARG* 1.3 75.5 - - - +
95R ALA* 1.3 58.0 + - - +
97R VAL* 4.0 1.0 - - - +
98R THR* 2.8 46.1 + - - +
65Y LEU* 4.2 17.0 - - + +
69Y ARG* 4.4 3.1 + - - -
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Residues in contact with ALA 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R HIS* 3.0 21.7 + - + +
92R ALA* 3.7 4.5 - - - +
93R ARG 3.2 0.2 - - - -
94R THR* 1.3 78.9 - - - +
96R ALA* 1.3 55.8 + - - +
98R THR* 4.0 4.5 - - - +
99R HIS* 3.0 28.4 + - - +
107R ILE* 4.0 7.4 - - + +
112R LEU* 4.2 10.3 - - + -
115R SER* 3.8 23.3 - - - +
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Residues in contact with ALA 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ILE* 4.5 5.8 - - + +
71R ASP* 4.0 30.5 - - + +
74R ILE* 5.4 0.2 - - + -
92R ALA 3.0 16.3 + - - +
93R ARG 3.2 3.6 + - - +
95R ALA* 1.3 72.7 - - - +
97R VAL* 1.3 66.4 + - - +
99R HIS* 3.4 4.7 + - - +
100R ASN* 3.1 22.1 + - - +
107R ILE* 3.9 30.3 + - + +
112R LEU* 4.2 5.1 - - + +
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Residues in contact with VAL 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R ASP* 4.8 6.3 - - - +
93R ARG 2.9 15.3 + - - +
94R THR 4.1 1.6 - - - +
96R ALA* 1.3 74.0 - - + +
98R THR* 1.3 60.8 + - - +
100R ASN* 2.9 9.5 + - - +
101R LEU* 2.8 26.7 + - + +
61Y SER* 3.7 36.9 + - - +
62Y GLN* 5.4 0.9 - - - +
64Y ARG* 3.6 30.5 - - + -
65Y LEU* 3.7 29.6 - - + -
68Y LEU* 4.5 7.4 - - + -
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Residues in contact with THR 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R THR* 2.8 38.9 + - - +
95R ALA* 4.0 5.4 - - - -
97R VAL* 1.3 74.0 - - - +
99R HIS* 1.3 64.9 + - - +
101R LEU* 3.1 10.8 + - + +
102R TYR* 2.8 57.4 + - + +
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Residues in contact with HIS 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R ALA 3.0 19.4 + - - +
96R ALA 3.6 4.9 - - - +
97R VAL 3.2 0.2 - - - -
98R THR* 1.3 78.2 - - - +
100R ASN* 1.3 58.1 + - - +
102R TYR* 4.8 0.9 - - - -
103R TYR* 2.9 53.6 + + - +
105R GLU* 3.1 36.4 + - + +
106R ASP 4.2 0.2 + - - -
107R ILE* 3.7 40.6 - - + +
108R ASN 5.2 0.4 + - - -
66Z TYR* 4.4 1.1 - + - -
70Z HIS* 3.1 40.7 + + - -
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Residues in contact with ASN 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R ASP* 5.8 3.6 - - - +
96R ALA 3.1 11.8 + - - +
97R VAL* 2.9 12.2 + - - +
99R HIS* 1.3 77.4 - - - +
101R LEU* 1.3 59.7 + - - +
104R ASP* 2.8 33.8 + - - +
105R GLU* 3.1 41.3 + - - +
106R ASP* 4.8 5.1 + - - +
61Y SER* 5.1 3.8 + - - -
81Z ARG* 3.5 4.0 + - - -
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Residues in contact with LEU 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R VAL 2.8 8.9 + - - +
98R THR* 3.4 12.3 - - + +
100R ASN* 1.3 78.1 + - - +
102R TYR* 1.3 66.1 + - + +
54Y PHE* 5.4 1.6 - - + +
57Y THR* 3.7 27.4 - - + -
58Y TRP* 3.9 39.7 - - + +
61Y SER* 3.5 27.8 + - - +
62Y GLN* 5.8 0.4 - - - +
81Z ARG* 2.9 29.2 + - - +
85Z HIS* 3.2 26.8 - - + +
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Residues in contact with TYR 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R THR* 2.8 44.8 + - + +
99R HIS* 5.6 0.2 - - - -
101R LEU* 1.3 83.1 - - + +
103R TYR* 1.3 87.2 + + + +
81Z ARG* 3.5 11.9 - - - +
82Z ASN* 3.5 22.3 + - - +
85Z HIS* 3.6 38.4 - + + +
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Residues in contact with TYR 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99R HIS* 2.9 46.0 + + - +
102R TYR* 1.3 101.5 - + + +
104R ASP* 1.3 69.8 + - - +
105R GLU* 3.2 17.7 + - + +
62Z SER* 4.7 7.9 + - - -
66Z TYR* 3.6 35.4 - + + +
70Z HIS* 4.8 6.5 - + - -
74Z LEU* 4.2 13.7 - - + -
78Z SER* 2.7 36.8 + - - -
81Z ARG* 4.1 4.3 - - - -
82Z ASN* 4.2 22.8 + - + -
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Residues in contact with ASP 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100R ASN* 2.8 29.7 + - - +
102R TYR 3.9 0.4 - - - -
103R TYR* 1.3 72.1 - - - +
105R GLU* 1.3 58.5 + - - +
77Z ASN* 3.0 38.8 + - - +
81Z ARG* 3.8 38.0 + - + +
119Z TYR* 5.3 2.3 + - - +
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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