Contacts of the helix formed by residues 132 - 149 (chain G) in PDB entry 2GTL
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 ASP 132 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A TYR* 4.5 8.6 - - - -
12A ARG* 3.0 30.2 + - - -
84A LEU 4.6 0.2 - - - +
85A ASP* 4.3 12.8 - - - +
87A THR* 3.3 14.1 + - - +
14G ILE* 4.1 8.7 - - + -
18G GLN* 3.1 22.6 - - - +
131G TYR* 1.3 71.5 - - - +
133G ALA* 1.3 66.3 + - - +
135G ALA* 2.8 45.2 + - + +
136G TRP* 3.1 13.7 + - - -
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Residues in contact with ALA 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A THR* 3.2 18.8 + - - -
88A LEU* 4.6 11.0 - - + +
91A GLN* 4.2 19.5 - - - +
131G TYR* 3.4 31.3 + - + +
132G ASP* 1.3 71.6 - - - +
134G LEU* 1.3 59.1 + - + +
136G TRP* 3.8 0.7 - - - +
137G LYS* 2.9 35.0 + - - +
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Residues in contact with LEU 134 (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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7A CYS* 4.7 16.2 - - + +
12A ARG* 3.6 40.4 - - - +
84A LEU* 4.7 3.8 - - + +
87A THR* 3.2 18.5 - - + +
90A LEU* 4.4 19.5 - - + -
141A ARG* 3.6 46.0 - - + +
11G ASP* 5.8 0.2 - - - -
132G ASP 3.0 1.0 + - - -
133G ALA* 1.3 80.2 - - + +
135G ALA* 1.3 64.6 + - - +
137G LYS* 4.0 4.2 - - + +
138G SER* 2.9 27.9 + - - -
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Residues in contact with ALA 135 (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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9A TYR* 5.3 0.4 - - + -
12A ARG* 3.8 1.7 - - - +
11G ASP* 3.7 43.3 - - - +
14G ILE* 4.3 8.3 - - + -
15G VAL* 4.0 7.2 - - + -
132G ASP* 2.8 30.9 + - + +
134G LEU* 1.3 73.6 - - - +
136G TRP* 1.3 65.7 + - + +
138G SER* 3.2 4.0 + - - -
139G CYS* 3.1 23.9 + - - -
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Residues in contact with TRP 136 (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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15G VAL* 3.5 51.3 - - + +
18G GLN* 2.7 31.4 - - - +
19G TRP* 3.6 39.9 - + + -
78G LEU* 5.8 0.9 - - + -
82G ILE* 4.1 12.3 - - + -
124G LEU* 3.4 24.9 - - + -
128G LEU* 4.2 9.9 - - + -
131G TYR* 3.3 39.7 - + + +
132G ASP* 3.1 11.0 + - + -
133G ALA 3.8 2.9 - - - +
135G ALA* 1.3 80.1 - - + +
137G LYS* 1.3 56.4 + - - +
139G CYS* 2.9 3.6 + - + +
140G LEU* 2.7 61.7 + - + +
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Residues in contact with LYS 137 (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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141A ARG* 4.5 21.4 - - - +
121G ALA* 6.1 7.0 - - + -
131G TYR* 4.8 1.5 + - - +
133G ALA 2.9 21.5 + - - +
134G LEU* 4.0 5.6 - - + +
136G TRP* 1.3 72.3 - - - +
138G SER* 1.3 65.4 + - - +
140G LEU* 4.1 7.1 - - - +
141G LYS* 3.0 32.5 + - + +
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Residues in contact with SER 138 (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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6A CYS* 4.6 12.0 - - - +
7A CYS 4.8 6.9 + - - -
6G CYS* 4.5 15.5 - - - +
7G CYS* 3.6 29.4 + - - +
11G ASP* 4.2 8.6 + - - -
134G LEU 2.9 16.4 + - - -
135G ALA 3.2 10.1 - - - -
136G TRP 3.1 1.0 - - - -
137G LYS* 1.3 81.0 - - - +
139G CYS* 1.3 60.8 + - - +
141G LYS* 3.6 5.3 - - - +
142G GLY* 3.5 13.7 + - - -
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Residues in contact with CYS 139 (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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7G CYS* 2.0 53.5 - - - -
11G ASP 4.4 0.7 - - - -
12G HIS* 3.9 19.7 - - - -
15G VAL* 3.9 18.2 - - + -
85G LEU* 4.6 11.0 - - + -
135G ALA 3.1 10.4 + - - +
136G TRP 2.9 6.9 + - - +
138G SER* 1.3 75.5 - - - +
140G LEU* 1.3 68.3 + - + +
141G LYS 3.0 2.3 + - - -
142G GLY* 3.1 3.9 + - - +
143G ILE* 3.0 27.0 + - + +
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Residues in contact with LEU 140 (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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78G LEU* 4.2 18.6 - - + -
82G ILE* 5.7 0.9 - - + -
117G GLY* 5.1 2.0 - - - +
120G LEU* 3.8 38.1 - - + -
121G ALA* 4.9 11.7 - - + +
124G LEU* 4.0 9.6 - - + -
131G TYR* 5.1 0.4 - - - +
136G TRP* 2.7 57.3 + - + +
137G LYS* 4.1 5.4 - - - +
139G CYS* 1.3 72.3 - - + +
141G LYS* 1.3 56.7 + - - +
143G ILE* 3.2 11.5 + - + +
144G LEU* 2.8 47.5 + - + +
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Residues in contact with LYS 141 (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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5A ASP* 5.7 2.8 + - - -
6A CYS* 6.0 0.6 - - - -
6G CYS* 5.1 16.3 - - - -
137G LYS* 3.0 24.9 + - + +
138G SER* 3.6 6.5 - - - +
139G CYS 3.0 0.2 - - - -
140G LEU* 1.3 76.4 - - - +
142G GLY* 1.3 66.5 + - - +
143G ILE 3.0 0.5 + - - -
144G LEU* 3.9 5.3 - - - +
145G THR* 2.9 37.7 + - - +
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Residues in contact with GLY 142 (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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7G CYS* 6.2 1.1 - - - -
95G LEU* 5.3 0.2 - - - -
138G SER 3.5 6.6 + - - -
139G CYS* 3.1 6.9 + - - -
141G LYS* 1.3 81.3 - - - +
143G ILE* 1.3 60.6 + - - +
145G THR* 3.9 4.6 - - - -
146G LYS* 3.2 39.3 + - - +
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Residues in contact with ILE 143 (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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78G LEU* 4.7 13.2 - - + -
81G ALA* 3.8 30.7 - - + -
82G ILE* 4.5 8.1 - - + +
85G LEU* 4.5 20.2 - - + -
91G LEU* 5.3 1.3 - - + -
95G LEU* 3.6 33.0 - - + -
139G CYS* 3.0 18.6 + - + +
140G LEU* 3.5 12.6 - - + +
141G LYS 3.1 0.2 - - - -
142G GLY* 1.3 73.9 - - - +
144G LEU* 1.3 68.3 + - + +
145G THR 3.1 0.7 + - - -
146G LYS* 3.2 4.2 + - - +
147G ILE* 3.0 35.9 + - + +
160G HEM 4.8 7.4 - - + -
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Residues in contact with LEU 144 (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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113G PHE* 3.5 31.4 - - + +
114G LYS* 5.9 0.7 - - - -
116G PHE* 4.1 12.8 - - + -
117G GLY* 3.5 32.8 - - - +
120G LEU* 5.3 4.5 - - + -
140G LEU* 2.8 37.4 + - + +
141G LYS* 4.0 4.7 - - - +
143G ILE* 1.3 75.4 - - + +
145G THR* 1.3 63.2 + - - +
147G ILE* 3.3 2.7 + - - +
148G SER* 3.1 23.5 + - - -
160G HEM 3.3 34.1 - - + -
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Residues in contact with THR 145 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141G LYS* 2.9 32.8 + - - +
142G GLY* 3.9 5.2 - - - -
144G LEU* 1.3 76.4 - - - +
146G LYS* 1.3 67.4 + - + +
147G ILE 3.0 0.9 + - - -
148G SER* 3.0 8.9 + - - -
149G SER* 3.0 25.7 + - - -
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Residues in contact with LYS 146 (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 LEU* 5.9 4.3 - - - +
92G ASP* 4.0 27.3 + - - +
95G LEU* 4.2 34.3 - - + +
96G ASP* 5.0 5.3 - - + +
99G ALA* 3.8 8.5 - - - +
142G GLY* 3.2 22.1 + - - +
143G ILE 3.2 4.2 + - - +
145G THR* 1.3 81.9 - - + +
147G ILE* 1.3 58.3 + - - +
149G SER* 2.8 24.7 + - - +
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Residues in contact with ILE 147 (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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95G LEU* 3.4 23.1 - - + -
98G LEU* 3.8 34.7 - - + +
99G ALA* 3.0 27.7 - - - +
102G HIS* 4.3 12.7 - - + +
113G PHE* 3.4 22.4 - - + -
143G ILE* 3.0 30.9 + - + +
144G LEU* 3.6 7.4 - - - +
145G THR 3.0 0.2 - - - -
146G LYS* 1.3 79.4 - - - +
148G SER* 1.3 57.7 + - - +
150G ARG 4.8 0.9 + - - +
160G HEM 3.8 33.0 - - + -
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Residues in contact with SER 148 (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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102G HIS* 5.9 0.7 - - - -
110G LYS* 3.9 20.5 - - - +
113G PHE* 3.7 32.2 - - - +
144G LEU 3.1 11.5 + - - -
145G THR* 3.0 8.0 + - - -
147G ILE* 1.3 76.7 - - - +
149G SER* 1.3 52.5 + - - +
150G ARG 2.5 19.9 + - - -
151G LEU* 3.4 35.1 - - - +
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Residues in contact with SER 149 (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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96G ASP* 5.6 1.4 + - - -
99G ALA* 4.4 5.4 - - - +
110G LYS* 4.8 11.9 - - - +
145G THR* 3.0 16.0 + - - -
146G LYS* 2.8 27.4 + - - +
147G ILE 3.4 1.0 - - - -
148G SER* 1.3 73.5 - - - +
150G ARG* 1.3 64.7 + - - +
151G LEU 4.2 0.4 - - - -
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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