Contacts of the helix formed by residues 108 - 126 (chain U) 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 PRO 108 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U ILE* 3.9 0.7 - - - -
99U PHE* 3.9 16.2 - - + -
105U TYR* 4.1 10.8 - - + +
106U ASP 3.1 8.7 - - - +
107U MET* 1.3 91.7 - - + +
109U CYS* 1.3 64.7 - - - +
110U ASP* 3.8 3.1 - - - +
111U VAL* 3.2 15.4 + - + -
112U LEU* 3.1 19.9 + - - +
142U ASP* 3.2 22.2 - - - +
72V ARG* 3.4 36.8 - - - +
75V ARG* 6.2 0.2 - - - +
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Residues in contact with CYS 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74U ILE* 3.7 17.4 - - + +
108U PRO* 1.3 73.3 - - - +
110U ASP* 1.3 59.4 + - - +
112U LEU* 3.5 3.3 + - - +
113U ALA* 2.9 25.8 + - - +
138U PHE* 3.5 42.9 - - - +
139U VAL* 3.9 6.7 - - - -
140U SER* 3.2 28.2 + - - +
142U ASP* 4.0 4.7 + - + +
147U SER* 4.4 9.2 - - - -
149U TYR* 3.9 14.8 - - - -
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Residues in contact with ASP 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108U PRO* 3.8 2.9 - - - +
109U CYS* 1.3 75.5 + - - +
111U VAL* 1.3 64.2 + - - +
113U ALA* 3.6 1.7 - - - +
114U LYS* 2.9 29.1 + - - +
142U ASP* 4.6 1.7 - - - +
144U LEU* 3.7 16.0 - - - +
147U SER* 5.4 0.3 + - - -
149U TYR* 3.5 40.2 - - + -
157U TYR* 4.0 6.7 + - + +
70V THR 4.2 3.3 - - - +
71V SER* 5.6 2.1 - - - -
72V ARG* 3.0 42.4 + - - -
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Residues in contact with VAL 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U PHE* 4.1 16.4 - - + -
107U MET* 4.4 5.8 - - + -
108U PRO* 3.2 22.2 + - + +
110U ASP* 1.3 77.5 - - - +
112U LEU* 1.3 59.6 + - - +
114U LYS* 3.3 6.8 + - - +
115U ARG* 2.8 28.6 + - + +
69V TYR* 4.1 19.9 - - + +
70V THR* 3.7 39.0 - - + -
72V ARG* 3.7 25.6 - - - +
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Residues in contact with LEU 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U ILE* 3.7 28.9 - - + -
74U ILE* 4.1 14.8 - - + -
92U ALA* 4.0 16.2 - - + +
95U GLU* 4.3 6.3 - - + -
107U MET* 3.5 35.8 - - + -
108U PRO 3.1 10.7 + - - +
109U CYS 3.7 7.0 - - - +
111U VAL* 1.3 75.0 - - - +
113U ALA* 1.3 64.5 + - - +
115U ARG* 4.3 4.0 - - + -
116U MET* 2.9 38.6 + - + +
138U PHE* 3.8 27.8 - - + -
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Residues in contact with ALA 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109U CYS 2.9 14.6 + - - +
110U ASP 3.6 8.5 - - - +
111U VAL 3.3 0.2 - - - -
112U LEU* 1.3 73.4 - - - +
114U LYS* 1.3 54.6 + - - +
116U MET* 3.1 3.1 + - - -
117U ALA* 2.8 34.1 + - - +
138U PHE* 4.0 17.0 - - + -
149U TYR* 3.6 26.2 - - + -
151U THR* 3.5 15.3 - - + +
157U TYR* 3.9 11.7 - - + -
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Residues in contact with LYS 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ARG* 4.4 15.5 - - - +
90O ASP* 3.2 37.4 + - - -
93O ARG* 4.6 5.7 - - - +
110U ASP 2.9 18.2 + - - +
111U VAL* 3.6 5.6 - - - +
113U ALA* 1.3 74.8 - - - +
115U ARG* 1.3 63.6 + - - +
117U ALA* 3.3 2.4 + - - +
118U ASN* 3.0 31.6 + - - +
157U TYR* 3.6 35.3 - - + +
68V LEU 4.6 0.8 + - - -
69V TYR* 3.4 49.9 + - + +
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Residues in contact with ARG 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U ARG* 3.4 15.4 - - - +
95U GLU* 2.9 50.8 + - + +
107U MET* 5.3 5.8 - - - -
111U VAL* 2.8 20.8 + - + +
112U LEU* 3.7 9.6 - - + +
113U ALA 3.2 0.2 - - - -
114U LYS* 1.3 73.7 - - - +
116U MET* 1.3 61.8 + - - +
118U ASN* 3.3 8.7 + - - +
119U LEU* 3.1 42.8 + - + +
122U ILE* 6.1 0.4 - - - +
69V TYR* 3.5 24.4 + - + +
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Residues in contact with MET 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88U ALA* 3.3 40.8 - - + +
91U ARG* 4.2 19.3 - - + -
92U ALA* 4.0 20.0 - - + -
95U GLU* 4.8 3.8 - - - -
112U LEU* 2.9 31.1 + - + +
113U ALA 3.8 2.5 - - - +
115U ARG* 1.3 71.9 - - - +
117U ALA* 1.3 68.1 + - - +
119U LEU* 3.2 15.3 + - + +
120U SER* 2.9 26.0 + - - +
132U LEU* 6.2 1.6 - - + -
136U LEU* 4.3 14.8 - - + -
138U PHE* 3.9 23.8 - - + -
151U THR* 4.7 2.7 - - - +
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Residues in contact with ALA 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ARG* 3.4 19.7 - - - +
113U ALA 2.8 16.7 + - - +
114U LYS 3.3 9.2 - - - +
116U MET* 1.3 72.0 - - - +
118U ASN* 1.3 50.1 + - - +
120U SER* 3.1 9.9 + - - -
121U GLN* 2.8 30.8 + - - +
151U THR* 4.3 8.8 - - + +
155U GLY* 3.4 18.9 - - - +
156U TYR 4.5 0.4 - - - +
157U TYR* 3.9 21.1 - - + -
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Residues in contact with ASN 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ARG* 2.7 46.6 - - - +
87O VAL* 3.6 20.1 - - + +
90O ASP* 3.9 7.0 + - - +
114U LYS* 3.0 24.8 + - - +
115U ARG* 3.7 13.7 - - - +
116U MET 3.3 0.4 - - - -
117U ALA* 1.3 70.6 - - - +
119U LEU* 1.3 67.1 + - - +
121U GLN* 3.3 8.2 + - - +
122U ILE* 3.2 26.5 + - + +
69V TYR* 3.2 25.8 + - - +
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Residues in contact with LEU 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U ARG* 3.5 48.5 - - + +
95U GLU* 4.2 5.4 - - - +
115U ARG* 3.1 47.2 + - - +
116U MET* 3.2 21.7 + - + +
118U ASN* 1.3 77.9 - - - +
120U SER* 1.3 62.9 - - - +
122U ILE* 3.1 27.5 + - + +
123U TYR* 3.4 37.8 - - + +
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Residues in contact with SER 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116U MET* 2.9 12.4 + - - +
117U ALA* 3.3 10.5 - - - -
119U LEU* 1.3 73.4 - - - +
121U GLN* 1.3 66.2 + - - +
123U TYR* 2.9 31.5 + - - +
124U THR* 3.2 13.2 + - - -
131U PRO* 5.7 0.3 - - - +
132U LEU* 5.5 6.2 + - - +
136U LEU* 5.7 4.0 - - - +
151U THR* 5.2 3.6 + - - -
152U ASP 4.0 20.9 + - - -
153U PRO* 4.4 9.9 - - - +
155U GLY* 4.1 4.9 - - - -
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Residues in contact with GLN 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O PRO* 3.5 32.5 - - + +
84O ASP* 3.1 18.4 - - - +
86O ARG* 4.4 0.9 - - - +
87O VAL* 3.5 29.2 - - + +
130O ARG* 4.2 0.3 + - - -
117U ALA 2.8 16.1 + - - +
118U ASN* 3.4 13.4 + - - +
120U SER* 1.3 72.5 - - - +
122U ILE* 1.3 74.8 + - - +
124U THR* 2.8 29.5 - - + -
125U GLN* 2.8 32.5 + - - +
155U GLY* 3.9 9.8 - - - -
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Residues in contact with ILE 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115U ARG* 6.1 0.4 - - - +
118U ASN* 3.2 15.1 + - + +
119U LEU* 3.1 26.4 + - + +
121U GLN* 1.3 87.4 - - - +
123U TYR* 1.3 69.2 + - + +
125U GLN* 2.9 5.0 + - - +
126U ARG* 2.8 56.3 + - + +
129U MET* 5.6 2.9 - - + -
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Residues in contact with TYR 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U THR* 3.3 4.5 + - - +
87U ASN* 5.7 1.9 + - - -
91U ARG* 4.9 7.1 + - - +
119U LEU* 3.4 44.4 - - + +
120U SER* 2.9 16.0 + - - +
122U ILE* 1.3 85.8 - - + +
124U THR* 1.3 60.2 + - - +
125U GLN 3.3 0.5 + - - -
126U ARG 3.4 0.4 - - - +
129U MET* 3.1 45.9 - - + +
130U ARG 3.6 26.2 - - - +
131U PRO* 3.8 17.6 - - + +
132U LEU* 4.2 28.6 - - + +
301U MG 2.4 30.6 - - - -
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Residues in contact with THR 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O MET* 4.7 3.1 - - + -
84O ASP* 4.2 5.2 - - - +
130O ARG* 2.7 53.5 + - - +
13U THR* 3.3 22.8 - - - -
21U LEU* 4.0 12.8 - - + +
24U VAL* 3.9 11.7 - - + +
120U SER 3.2 5.4 + - - -
121U GLN* 2.8 19.1 - - + +
123U TYR* 1.3 76.4 - - - +
125U GLN* 1.3 54.6 + - - -
131U PRO* 4.9 1.4 - - - +
153U PRO 3.5 15.2 + - - -
154U ALA* 3.4 22.5 + - - +
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Residues in contact with GLN 125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O LEU* 5.8 0.2 - - - +
84O ASP* 4.5 0.6 + - - -
87O VAL* 4.9 0.6 - - - +
123O ALA* 4.1 3.2 - - - +
129O VAL* 3.5 12.8 - - + -
130O ARG* 3.0 62.0 + - + +
132O PHE* 3.5 46.7 + - - -
13U THR* 4.3 2.9 + - - +
121U GLN* 2.8 33.8 + - - +
122U ILE* 2.9 8.9 + - - +
124U THR* 1.3 81.0 - - - +
126U ARG* 1.3 63.8 + - + +
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Residues in contact with ARG 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126O SER* 5.8 3.8 - - - -
127O GLY 4.6 6.3 + - - -
128O GLY 3.4 7.4 + - - +
129O VAL* 3.8 25.8 - - + +
13U THR* 4.0 0.9 - - - -
122U ILE* 2.8 39.3 + - + +
123U TYR 3.4 1.4 - - - +
125U GLN* 1.3 77.5 - - + +
127U ALA* 1.3 56.9 + - - +
128U TYR* 3.4 33.3 + - + -
129U MET* 3.5 7.9 + - + +
301U MG 2.3 31.1 - - - -
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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
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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) + - + + + + + -
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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