Contacts of the helix formed by residues 138 - 147 (chain G) in PDB entry 1GLE
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 GLY 138 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G PHE 3.4 1.8 + - - -
137G SER* 1.3 66.4 - - - +
139G THR* 1.3 53.7 + - - +
141G VAL* 2.5 36.6 + - - +
142G LYS 3.2 2.8 + - - -
189G THR 2.6 21.8 + - - -
190G MET* 4.6 5.6 - - - +
191G LEU* 4.1 16.1 - - - +
207G LEU* 3.4 22.1 - - - +
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Residues in contact with THR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G THR* 3.0 32.2 + - - +
111G ILE* 3.8 26.5 - - + +
112G CYS* 4.4 10.2 - - - -
115G LEU* 4.0 21.3 - - + -
133G ASP 4.8 0.9 + - - -
134G PRO* 4.2 6.9 - - - +
136G PHE 3.8 10.1 + - - -
138G GLY* 1.3 67.5 - - - +
140G LYS* 1.3 65.7 + - - +
142G LYS* 3.8 5.8 - - - +
143G TRP* 2.8 27.0 + - - +
190G MET* 4.9 7.9 - - + +
207G LEU* 3.5 10.3 - - + +
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Residues in contact with LYS 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLU* 4.5 3.6 - - - +
86G THR* 3.4 28.0 - - + +
101G ILE* 3.3 35.5 - - + +
102G VAL 2.4 31.0 + - - -
103G TRP* 3.1 15.6 + - - +
105G CYS 3.6 10.0 + - - +
108G THR* 3.8 15.5 - - + -
134G PRO 3.0 26.3 + - - +
135G TYR 3.3 13.7 - - - -
136G PHE 3.7 11.0 - - - +
137G SER 2.9 7.7 + - - +
139G THR* 1.3 72.0 + - - +
141G VAL* 1.3 67.0 + - - +
143G TRP* 3.8 1.9 - - - +
144G ILE* 3.1 23.6 + - - +
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Residues in contact with VAL 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G THR* 3.7 9.6 - - + -
88G VAL* 5.0 6.3 - - + -
137G SER 2.9 7.7 + - - +
138G GLY* 2.5 20.7 + - - +
140G LYS* 1.3 71.8 - - - +
142G LYS* 1.3 54.3 + - - +
144G ILE* 2.8 22.1 + - - +
145G LEU* 2.9 23.7 + - + +
162G PHE* 3.0 46.4 - - + -
191G LEU* 5.2 2.9 - - + -
209G ILE* 3.1 37.2 - - + -
213G MET* 4.9 5.8 - - - -
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ILE* 4.2 28.4 - - + +
114G HIS* 5.6 5.3 + - - -
138G GLY 3.2 6.3 + - - +
139G THR* 3.9 9.2 - - - +
141G VAL* 1.3 78.2 - - - +
143G TRP* 1.3 64.1 + - - +
145G LEU* 4.4 7.6 - - - -
146G ASP* 2.7 59.4 + - - +
152G ARG* 3.9 12.3 - - - +
206G VAL 5.5 3.0 + - - -
207G LEU* 4.0 32.1 - - + +
208G ASP* 5.5 0.9 - - - -
209G ILE* 4.0 4.9 - - + +
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Residues in contact with TRP 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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44G TRP* 3.8 23.5 - + - -
98G TYR* 3.5 48.0 - + - -
101G ILE* 4.3 8.1 - - + -
107G ARG* 3.6 39.3 + - + +
108G THR* 3.6 11.0 - - + -
111G ILE* 4.0 18.8 - - + -
139G THR 2.8 22.1 + - - +
140G LYS* 3.8 3.1 - - - +
142G LYS* 1.3 77.2 - - - +
144G ILE* 1.3 70.8 + - + +
146G ASP* 3.1 6.6 + - - -
147G HIS* 3.0 68.3 + + + -
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Residues in contact with ILE 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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86G THR* 4.2 16.6 - - + +
87G ILE* 5.0 1.6 - - - -
88G VAL* 3.4 33.2 - - + +
97G ILE* 3.5 33.0 - - + -
98G TYR* 4.2 25.3 - - + -
99G ASN 4.7 8.3 - - - +
101G ILE* 5.1 7.0 - - + -
140G LYS 3.1 12.5 + - - +
141G VAL 2.8 9.8 + - - +
143G TRP* 1.3 87.9 - - + +
145G LEU* 1.3 69.3 + - + +
147G HIS 3.0 20.1 + - - +
148G VAL* 3.7 5.6 + - + +
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Residues in contact with LEU 145 (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 VAL* 5.3 3.1 - - + -
97G ILE* 5.2 2.0 - - + -
141G VAL* 2.9 30.6 + - + +
142G LYS* 3.8 5.6 - - - +
144G ILE* 1.3 81.0 - - + +
146G ASP* 1.3 60.6 + - - +
147G HIS 3.4 0.5 + - - -
148G VAL 3.4 17.2 - - - +
151G SER* 3.5 42.3 - - - +
152G ARG* 3.1 37.9 + - + +
155G ALA* 4.7 0.4 - - + -
160G LEU* 4.6 5.8 - - + -
208G ASP 3.8 16.2 - - - +
209G ILE* 4.5 1.8 - - + -
210G PRO* 4.3 11.2 - - + -
213G MET* 4.6 17.0 - - + -
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Residues in contact with ASP 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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111G ILE* 5.7 1.6 - - - +
142G LYS* 2.7 54.3 + - - +
143G TRP* 3.3 8.4 - - - +
144G ILE 3.0 0.2 - - - -
145G LEU* 1.3 79.5 - - - +
147G HIS* 1.4 67.0 + - + +
148G VAL 3.6 2.8 + - - +
152G ARG* 3.4 18.2 + - - -
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Residues in contact with HIS 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G TYR* 5.0 7.1 - - + -
143G TRP* 3.0 80.7 + + + +
144G ILE 3.0 6.4 + - - +
146G ASP* 1.4 85.4 - - + +
148G VAL* 1.3 70.7 - - - +
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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
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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