Contacts of the helix formed by residues 108 - 126 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ILE* 4.0 0.9 - - - -
99G PHE* 4.0 12.3 - - + -
105G TYR* 4.2 7.0 - - + +
106G ASP 3.4 9.6 - - - +
107G MET* 1.3 91.0 - - + +
109G CYS* 1.3 54.0 + - - +
110G ASP* 3.3 5.8 - - - +
111G VAL* 3.0 16.8 + - + +
112G LEU* 2.9 32.2 + - - +
142G ASP* 3.3 23.6 - - - +
72H ARG* 3.4 39.7 - - - +
75H ARG* 6.2 0.7 - - - +
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Residues in contact with CYS 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ILE* 3.6 19.7 - - - +
108G PRO* 1.3 69.8 - - - +
110G ASP* 1.3 60.2 + - - +
112G LEU* 3.4 2.3 + - - +
113G ALA* 2.9 29.9 + - - +
138G PHE* 3.5 43.3 - - - +
139G VAL* 3.8 8.1 - - - -
140G SER* 3.2 29.0 + - - +
142G ASP* 4.5 3.9 + - + +
147G SER* 4.2 16.2 - - - -
149G TYR* 4.3 5.8 - - - -
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Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G PRO* 3.5 4.7 - - - +
109G CYS* 1.3 76.6 + - - +
111G VAL* 1.3 58.9 + - - +
113G ALA* 3.3 2.8 - - - +
114G LYS* 2.7 34.9 + - - +
142G ASP* 4.3 2.6 - - - +
144G LEU* 4.1 14.4 - - - +
147G SER* 5.5 0.5 + - - -
149G TYR* 3.5 42.3 - - + -
157G TYR* 3.9 5.3 - - + +
70H THR 4.0 3.5 - - - +
71H SER* 5.3 2.8 - - - -
72H ARG* 2.8 43.8 + - - -
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Residues in contact with VAL 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G PHE* 4.0 18.6 - - + -
107G MET* 4.3 5.6 - - + -
108G PRO* 3.0 20.3 + - + +
110G ASP* 1.3 76.2 - - - +
112G LEU* 1.3 67.6 + - - +
114G LYS* 3.3 7.5 + - + +
115G ARG* 2.9 23.1 + - + +
69H TYR* 4.3 16.3 - - + +
70H THR* 3.7 39.3 - - + +
72H ARG* 3.6 26.0 - - - +
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Residues in contact with LEU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 3.7 24.9 - - + -
74G ILE* 3.9 16.4 - - + -
92G ALA* 4.0 16.2 - - + +
95G GLU* 4.3 7.9 - - + -
107G MET* 3.5 33.1 - - + -
108G PRO 2.9 12.4 + - - +
109G CYS 3.7 6.5 - - - +
111G VAL* 1.3 76.9 - - - +
113G ALA* 1.3 53.5 + - - +
115G ARG* 3.0 6.4 + - + +
116G MET* 2.8 50.4 + - + +
138G PHE* 3.7 32.5 - - + -
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Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G CYS 2.9 14.9 + - - +
110G ASP 3.3 9.0 - - - +
112G LEU* 1.3 76.3 - - - +
114G LYS* 1.3 64.0 + - - +
116G MET 3.3 0.3 + - - -
117G ALA* 2.9 20.4 + - - +
138G PHE* 4.1 18.1 - - + -
149G TYR* 3.7 25.1 - - + -
151G THR* 3.4 18.9 - - + +
157G TYR* 3.9 10.8 - - + -
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Residues in contact with LYS 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 4.3 15.5 - - - +
90A ASP* 3.3 34.4 + - - -
93A ARG* 4.8 4.4 - - - +
110G ASP 2.7 16.2 + - - +
111G VAL* 3.3 7.2 + - - +
113G ALA* 1.3 72.7 - - - +
115G ARG* 1.3 57.8 + - - +
117G ALA* 3.4 1.2 + - - +
118G ASN* 2.9 35.4 + - - +
157G TYR* 3.4 39.9 - - + +
68H LEU 4.6 2.4 + - - -
69H TYR* 3.0 54.0 + - + +
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Residues in contact with ARG 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ARG* 3.5 15.4 - - - +
95G GLU* 3.0 50.1 + - + +
107G MET* 5.3 4.7 - - - -
111G VAL* 2.9 15.0 + - + +
112G LEU* 3.4 11.7 - - + +
114G LYS* 1.3 74.6 - - - +
116G MET* 1.3 66.8 + - - +
118G ASN* 3.1 21.7 + - - +
119G LEU* 3.1 34.4 + - + +
122G ILE* 5.9 1.6 - - - +
69H TYR* 3.6 26.2 + - + +
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Residues in contact with MET 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G ALA* 3.6 33.0 - - + +
91G ARG* 4.1 22.9 - - + -
92G ALA* 4.1 16.8 - - + -
95G GLU* 4.8 4.3 - - - -
112G LEU* 2.8 31.6 + - + +
113G ALA 3.9 2.7 - - - +
115G ARG* 1.3 72.5 - - - +
117G ALA* 1.3 61.4 + - - +
119G LEU* 3.4 15.8 + - + +
120G SER* 3.1 23.7 + - - -
132G LEU* 6.1 1.8 - - + -
136G LEU* 4.3 23.2 - - + +
138G PHE* 3.9 22.0 - - + -
151G THR* 4.6 4.0 - - - +
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 3.3 21.5 + - - +
113G ALA 2.9 17.7 + - - +
114G LYS 3.5 4.0 - - - +
116G MET* 1.3 75.8 - - - +
118G ASN* 1.3 58.6 + - - +
120G SER* 3.1 6.7 + - - -
121G GLN 2.9 24.4 + - - -
151G THR* 3.9 17.4 - - + +
155G GLY* 3.4 21.2 - - - +
156G TYR 4.4 0.2 - - - +
157G TYR* 4.0 10.1 - - + -
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Residues in contact with ASN 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG* 2.7 40.5 - - - +
87A VAL* 4.1 14.8 - - + +
90A ASP* 3.0 23.9 - - - +
114G LYS* 2.9 18.8 + - - +
115G ARG* 3.1 19.9 + - - +
117G ALA* 1.3 76.6 - - - +
119G LEU* 1.3 61.9 + - - +
121G GLN* 3.5 7.8 + - - +
122G ILE* 3.2 26.2 + - + +
69H TYR* 3.6 16.6 + - - +
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Residues in contact with LEU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ARG* 3.6 47.3 - - + +
95G GLU* 4.2 5.6 - - - +
115G ARG* 3.1 43.8 + - + +
116G MET* 3.6 21.5 - - + +
117G ALA 3.2 0.4 - - - -
118G ASN* 1.3 76.0 - - - +
120G SER* 1.3 62.4 + - - +
122G ILE* 3.2 28.2 + - + +
123G TYR* 3.4 44.1 + - + +
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Residues in contact with SER 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G MET 3.1 13.8 + - - -
117G ALA* 3.1 11.5 + - - -
119G LEU* 1.3 74.0 - - - +
121G GLN* 1.3 66.0 + - - +
123G TYR* 2.9 29.2 + - - +
124G THR* 3.1 12.5 + - - -
132G LEU* 5.7 6.2 + - - +
136G LEU* 5.8 3.6 - - - +
151G THR* 5.6 1.9 + - - -
152G ASP 3.9 13.1 + - - -
153G PRO* 4.4 11.3 - - - +
155G GLY* 3.7 16.4 - - - -
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Residues in contact with GLN 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A PRO* 3.8 30.3 - - + +
84A ASP* 3.0 25.7 - - - +
86A ARG* 4.5 0.9 - - - +
87A VAL* 3.6 28.2 - - + +
130A ARG* 4.1 0.2 + - - -
117G ALA 2.9 12.2 + - - +
118G ASN* 3.5 9.0 - - - +
120G SER* 1.3 75.7 - - - +
122G ILE* 1.3 75.8 + - - +
124G THR* 2.8 30.7 + - + -
125G GLN* 2.6 38.2 + - - +
154G ALA 4.5 0.7 - - - -
155G GLY* 3.9 5.2 - - - -
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Residues in contact with ILE 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G ARG* 5.9 0.7 - - - +
118G ASN* 3.2 14.3 + - + +
119G LEU* 3.2 28.4 + - + +
120G SER 3.2 0.8 - - - -
121G GLN* 1.3 91.2 - - - +
123G TYR* 1.3 68.3 + - + +
125G GLN* 3.0 4.5 + - - +
126G ARG* 2.9 54.4 + - + +
129G MET* 5.3 3.1 - - + -
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Residues in contact with TYR 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G THR* 3.4 4.5 + - - +
87G ASN* 5.6 2.6 + - - -
91G ARG* 4.7 8.1 + - - +
119G LEU* 3.4 43.6 - - + +
120G SER* 2.9 17.4 + - - +
122G ILE* 1.3 85.3 - - + +
124G THR* 1.3 58.1 + - - +
126G ARG 4.7 0.2 - - - -
129G MET* 3.4 44.7 - - + +
130G ARG 3.9 14.6 - - - +
131G PRO* 3.9 26.3 - - + +
132G LEU* 4.4 26.7 - - + +
9001G MG 2.3 30.3 - - - -
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Residues in contact with THR 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A MET* 4.5 3.6 - - + -
83A PRO* 6.2 0.2 - - + -
84A ASP* 4.3 4.3 - - - +
130A ARG* 2.6 55.3 + - - +
13G THR* 3.3 24.1 - - - +
21G LEU* 4.0 11.9 - - + +
24G VAL* 3.4 19.7 - - - +
120G SER 3.1 3.9 + - - -
121G GLN* 2.8 21.5 - - + +
123G TYR* 1.3 78.6 - - - +
125G GLN* 1.3 55.7 + - - +
131G PRO* 5.2 0.4 - - - +
153G PRO 3.5 14.9 + - - -
154G ALA* 4.0 11.3 + - - +
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Residues in contact with GLN 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 5.7 0.2 - - - +
87A VAL* 5.0 0.4 - - - +
123A ALA* 4.2 3.7 - - - +
129A VAL* 3.4 11.1 - - + -
130A ARG* 3.1 68.7 + - + +
132A PHE* 3.3 46.6 + - - -
13G THR* 4.4 3.4 - - - +
121G GLN* 2.6 43.1 + - - +
122G ILE* 3.0 5.6 + - - +
124G THR* 1.3 80.6 - - - +
126G ARG* 1.3 65.2 + - + +
127G ALA 3.9 0.2 + - - -
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Residues in contact with ARG 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A SER* 6.0 2.2 - - - -
127A GLY 4.7 5.9 + - - -
128A GLY 3.5 6.2 + - - +
129A VAL* 3.7 27.1 - - + +
13G THR* 4.0 1.1 - - - -
122G ILE* 2.9 35.0 + - + +
123G TYR 3.6 1.0 - - - +
125G GLN* 1.3 80.9 - - + +
127G ALA* 1.3 58.1 + - - +
128G TYR* 3.4 32.4 + - + -
129G MET* 3.5 8.4 + - + +
9001G MG 2.3 31.2 - - - -
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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