Contacts of the helix formed by residues 108 - 124 (chain G) in PDB entry 5A0Q
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 LEU 108 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72G HIS* 5.0 3.0 - - - -
73G VAL* 3.7 20.6 - - + -
106G ILE 3.9 1.6 + - - -
107G PRO* 1.4 70.3 - - - +
109G LYS* 1.3 59.2 + - - +
111G LEU* 4.0 14.6 - - + -
112G ALA* 2.9 33.2 + - + +
137G LEU* 3.8 20.0 - - + +
138G GLY* 3.7 11.9 - - - +
139G SER* 3.7 27.1 - - - +
144G ASP* 5.1 4.0 + - - -
147G GLN* 3.4 47.1 - - + +
149G TYR* 3.8 16.8 - - + -
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Residues in contact with LYS 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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107G PRO* 4.2 16.4 - - + -
108G LEU* 1.3 78.6 - - - +
110G HIS* 1.4 57.5 + - + +
112G ALA* 4.3 0.7 - - - +
113G ASP* 3.0 31.8 + - - +
144G ASP* 3.8 21.7 - - - +
147G GLN* 5.5 5.6 - - + +
149G TYR* 4.4 27.9 - - + +
69H GLU 5.1 4.0 - - - -
70H LEU* 3.4 30.7 + - + +
71H ASN* 4.8 11.5 + - - +
72H GLU* 4.2 13.3 + - - +
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Residues in contact with HIS 110 (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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98G PHE* 3.4 34.7 - + - -
102G PHE* 5.7 1.0 - - - -
106G ILE* 4.6 5.8 - - + -
107G PRO* 3.4 21.8 + - + +
108G LEU 3.2 0.2 - - - -
109G LYS* 1.4 78.8 - - + +
111G LEU* 1.3 58.9 + - - +
112G ALA 3.3 1.8 - - - -
113G ASP* 3.3 9.8 + - - +
114G ARG* 3.0 62.0 + - + +
69H GLU* 4.2 29.0 + - + +
70H LEU* 4.2 17.0 - - + +
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Residues in contact with LEU 111 (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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69G VAL* 4.0 12.6 - - + -
73G VAL* 3.8 41.5 - - + -
91G ALA* 4.2 7.6 - - + +
94G GLU* 3.4 29.8 - - + +
95G ALA* 4.7 1.3 - - + +
106G ILE* 3.9 28.7 - - + -
107G PRO 3.0 16.5 + - - +
108G LEU* 3.1 12.3 + - + +
110G HIS* 1.3 74.2 - - - +
112G ALA* 1.3 65.2 + - - +
114G ARG* 4.6 2.5 - - + -
115G VAL* 3.1 28.7 + - + +
137G LEU* 4.3 8.1 - - + -
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Residues in contact with ALA 112 (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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108G LEU* 2.9 20.2 + - + +
111G LEU* 1.3 77.0 - - - +
113G ASP* 1.3 63.1 + - - +
116G ALA* 2.9 34.7 + - - +
137G LEU* 6.0 3.4 - - + -
149G TYR* 3.6 38.8 - - + -
151G ILE* 3.4 15.0 - - + +
157G SER* 4.3 8.3 - - - -
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Residues in contact with ASP 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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88A ARG* 6.2 2.0 - - - -
92A GLN* 6.2 1.6 - - - +
109G LYS 3.0 21.0 - - - +
110G HIS* 3.6 13.5 + - - +
112G ALA* 1.3 79.4 - - - +
114G ARG* 1.3 63.5 + - - +
116G ALA* 3.9 5.1 - - - +
117G MET* 3.1 26.9 + - - +
149G TYR* 4.9 5.4 - - - -
157G SER* 3.8 13.4 + - - -
69H GLU 5.5 3.1 - - - +
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Residues in contact with ARG 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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92A GLN* 3.6 36.1 + - - +
94G GLU* 3.9 25.4 - - + +
106G ILE* 6.0 1.6 - - + -
110G HIS* 3.0 51.9 + - + +
111G LEU* 3.9 6.5 - - + +
112G ALA 3.3 0.4 - - - -
113G ASP* 1.3 79.3 + - - +
115G VAL* 1.3 65.4 + - - +
117G MET* 3.2 33.3 + - - +
118G TYR* 3.2 18.0 + - - +
69H GLU* 5.0 2.0 + - - +
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Residues in contact with VAL 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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87G LEU* 4.6 15.5 - - + +
90G ILE* 5.4 2.7 - - + -
91G ALA* 4.0 13.5 - - + -
94G GLU* 2.1 43.7 - - - +
111G LEU* 3.1 27.3 + - + +
114G ARG* 1.3 74.0 - - - +
116G ALA* 1.3 57.3 + - - +
118G TYR* 3.2 5.2 + - - +
119G VAL* 2.9 28.3 + - + +
135G PHE* 3.8 33.0 - - + -
137G LEU* 5.0 2.2 - - + -
151G ILE* 4.0 6.3 - - + -
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Residues in contact with ALA 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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112G ALA 2.9 20.7 + - - +
113G ASP* 3.9 4.5 - - - +
115G VAL* 1.3 72.7 - - - +
117G MET* 1.3 59.3 + - - +
118G TYR 3.4 0.2 - - - -
119G VAL* 3.4 1.5 + - - -
120G HIS* 3.0 21.7 + - - +
151G ILE* 3.8 24.6 - - + +
155G GLY* 3.2 24.2 - - - +
157G SER* 3.7 19.3 - - - +
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Residues in contact with MET 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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88A ARG* 5.0 9.0 - - + +
89A SER* 3.8 40.2 - - - +
92A GLN* 5.4 9.9 - - + -
113G ASP 3.1 15.9 + - - +
114G ARG* 3.2 32.7 + - - +
116G ALA* 1.3 74.1 - - - +
118G TYR* 1.3 64.2 + - - +
120G HIS* 3.1 26.7 + - + +
121G ALA* 3.2 17.7 + - + +
124G LEU* 6.0 1.3 - - + -
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Residues in contact with TYR 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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86G SER* 6.0 1.3 - - - -
87G LEU* 4.1 16.4 - - + -
90G ILE* 3.9 46.1 - - + +
94G GLU* 4.2 8.5 - - - +
114G ARG 3.2 8.5 + - - +
115G VAL* 3.2 8.0 + - + +
117G MET* 1.3 81.3 - - - +
119G VAL* 1.3 60.9 + - - +
120G HIS 3.6 0.2 + - - -
121G ALA* 3.6 11.0 + - + +
122G TYR* 2.9 45.6 + + - -
131G PHE* 4.0 16.8 - + - -
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Residues in contact with VAL 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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87G LEU* 3.5 30.1 - - + -
115G VAL 2.9 20.8 + - - +
116G ALA* 3.5 10.1 - - - +
117G MET 3.2 0.2 - - - -
118G TYR* 1.3 74.4 - - - +
120G HIS* 1.4 60.8 + - - +
121G ALA 3.5 0.5 + - - -
122G TYR* 3.8 5.5 + - - +
123G THR* 4.2 1.9 - - - +
131G PHE* 3.3 28.4 - - + -
135G PHE* 4.3 7.6 - - + -
151G ILE* 4.3 10.5 - - + -
152G ASP 3.4 20.6 - - - +
153G PRO* 3.3 30.5 - - + +
155G GLY 3.7 4.3 - - - +
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Residues in contact with HIS 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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85A ALA* 3.3 35.3 + - + +
86A ASP* 3.6 18.8 - - - -
88A ARG* 5.7 0.7 - - + -
89A SER* 3.8 20.9 - - - -
134A LEU* 4.5 0.4 - - - +
116G ALA 3.0 14.7 + - - +
117G MET* 3.1 20.6 + - - +
119G VAL* 1.4 73.9 - - - +
121G ALA* 1.3 62.3 + - - +
122G TYR 3.2 0.9 - - - -
123G THR* 2.8 30.7 + - - -
124G LEU* 3.3 42.5 - - + +
154G SER 3.3 24.0 + - - +
155G GLY* 4.2 2.7 - - - +
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Residues in contact with ALA 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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117G MET* 3.2 15.5 + - + +
118G TYR* 3.8 16.2 - - + +
119G VAL 3.4 0.8 - - - -
120G HIS* 1.3 76.9 - - - +
122G TYR* 1.3 67.5 + - + +
124G LEU* 3.3 17.4 + - - +
125G TYR* 3.0 38.6 - - + +
128G VAL* 5.1 0.2 - - - -
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Residues in contact with TYR 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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121F GLN* 2.7 42.6 - - + +
11G ALA* 4.7 0.3 - - - +
118G TYR* 2.9 45.4 + + - -
119G VAL 4.0 2.5 - - - +
120G HIS 3.2 0.4 - - - -
121G ALA* 1.3 75.6 - - + +
123G THR* 1.3 64.7 + - - +
124G LEU 3.0 3.2 + - - -
125G TYR 3.2 19.6 + - - +
128G VAL* 3.4 39.6 - - + +
129G ARG 3.0 17.3 - - - +
130G PRO* 4.0 9.2 - - + +
131G PHE* 2.9 41.8 - + + -
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Residues in contact with THR 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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85A ALA* 5.5 0.2 - - - +
132A ARG* 3.2 22.7 + - - -
11G ALA* 4.1 13.7 - - - +
23G VAL* 4.1 27.4 - - + +
119G VAL 4.2 4.0 - - - +
120G HIS* 2.8 30.2 + - - +
122G TYR* 1.3 76.9 - - - +
124G LEU* 1.4 64.3 + - - +
125G TYR 3.7 0.8 + - - -
130G PRO* 4.3 15.5 - - + +
153G PRO 3.9 21.5 - - - +
154G SER* 4.0 16.6 - - - +
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Residues in contact with LEU 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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86A ASP* 4.0 0.2 - - - +
89A SER* 4.4 11.7 - - - +
131A MET* 3.9 0.9 - - - +
132A ARG* 3.4 42.0 + - - +
134A LEU* 3.3 35.0 - - + -
12G SER* 4.9 2.1 - - - -
117G MET* 6.0 1.1 - - + -
120G HIS* 3.3 50.5 - - + +
121G ALA* 3.6 12.1 - - - +
122G TYR 3.0 1.4 + - - -
123G THR* 1.4 82.6 - - - +
125G TYR* 1.3 87.2 + - + +
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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