Contacts of the helix formed by residues 139 - 152 (chain A) in PDB entry 3RLG
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 TYR 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ILE* 4.8 2.9 - - - -
135A ASP 4.2 0.4 + - - -
136A LEU 3.2 25.2 + - - +
137A ASN* 4.2 5.2 - - - -
138A HIS* 1.3 76.3 - - - +
140A PRO* 1.4 87.8 - - + +
141A LEU 3.0 0.2 - - - -
142A ILE* 3.0 24.4 + - + +
143A LYS* 4.1 1.0 + - - +
165A PHE* 3.8 24.6 - - + -
182A ALA* 4.2 9.6 - - + +
185A LYS* 4.0 42.2 + - + +
186A ALA* 3.8 27.1 - - + +
290A EDO 4.2 14.8 - - - -
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Residues in contact with PRO 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP 5.8 1.3 - - - +
102A ALA* 4.6 4.9 - - + -
103A ASN* 3.3 31.5 + - + +
137A ASN 3.4 12.1 - - - +
138A HIS* 3.1 7.0 - - - -
139A TYR* 1.4 115.1 - - + +
141A LEU* 1.3 60.4 + - - +
142A ILE 3.1 0.4 + - - -
143A LYS* 3.2 9.0 + - + +
144A GLY 3.1 17.5 + - - -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.9 28.5 - - + -
94A THR* 3.8 28.9 - - + -
102A ALA* 3.2 30.6 + - + +
103A ASN* 4.1 0.4 - - - +
105A ALA* 4.1 10.3 - - + -
106A GLY* 3.4 17.9 - - - +
109A LEU* 4.1 7.2 - - + -
131A LEU* 4.6 13.0 - - + -
133A ILE* 4.1 17.3 - - + -
138A HIS* 3.0 15.8 + - + +
139A TYR 3.0 0.4 + - - -
140A PRO* 1.3 77.2 - - - +
142A ILE* 1.3 60.5 + - - +
144A GLY 3.3 0.7 + - - -
145A PHE* 3.0 25.0 + - + +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 5.8 3.8 - - + -
133A ILE* 3.8 23.3 - - + -
139A TYR 3.0 16.2 + - - +
141A LEU* 1.3 79.8 - - + +
143A LYS* 1.3 58.6 + - - +
145A PHE* 3.2 7.3 + - + +
146A LYS* 2.9 28.7 + - + +
158A MET* 5.1 5.2 - - + -
163A HIS* 3.6 43.3 - - + +
165A PHE* 4.5 13.9 - - + -
183A TYR* 4.5 5.6 - - + -
186A ALA* 4.3 12.6 - - + +
188A ILE* 3.8 31.6 - - + -
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 4.2 10.1 - - - +
139A TYR 4.1 1.2 + - - +
140A PRO* 3.2 13.6 + - + +
142A ILE* 1.3 77.2 - - - +
144A GLY* 1.3 60.6 + - - +
146A LYS* 3.8 6.0 - - - +
147A ASP* 2.8 61.8 + - - +
186A ALA* 5.7 5.5 + - - +
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 3.3 35.5 - - - +
107A LYS* 3.3 23.2 - - - +
140A PRO 3.1 10.9 + - - -
141A LEU 3.7 1.1 - - - -
142A ILE 3.2 0.4 - - - -
143A LYS* 1.3 78.7 - - - +
145A PHE* 1.4 60.5 + - - +
147A ASP* 3.4 1.4 + - - +
148A GLN* 3.0 19.6 + - - +
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Residues in contact with PHE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY* 3.3 29.9 - - - +
109A LEU* 3.9 8.7 - - + -
110A ALA* 3.5 21.4 - - + +
113A LEU* 3.5 32.8 - - + -
118A TRP* 4.1 17.3 - + - -
129A ILE* 5.9 0.4 - - + -
131A LEU* 3.8 29.2 - - + -
141A LEU* 3.0 17.3 + - + +
142A ILE* 3.2 7.4 + - - +
144A GLY* 1.4 76.6 - - - +
146A LYS* 1.3 64.2 + - - +
148A GLN 3.3 0.2 + - - -
149A LEU* 3.1 40.4 + - + +
158A MET* 3.7 20.6 - - + -
161A VAL* 3.9 12.6 - - + -
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Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ILE* 2.9 18.3 + - + +
143A LYS* 3.9 5.8 - - - +
145A PHE* 1.3 77.6 - - - +
147A ASP* 1.3 67.6 + - - +
149A LEU* 3.3 4.0 + - - +
150A THR* 2.9 43.4 + - - +
155A PRO* 6.5 0.7 - - - -
158A MET* 4.1 38.8 - - + -
188A ILE* 6.2 3.8 - - + -
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Residues in contact with ASP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 5.4 0.9 + - - -
107A LYS* 5.1 9.7 - - - -
143A LYS* 2.8 59.7 + - - +
144A GLY* 4.0 4.6 - - - +
146A LYS* 1.3 85.1 + - - +
148A GLN* 1.3 57.3 + - - +
150A THR* 3.3 7.4 + - - -
151A LYS* 2.9 29.3 + - - +
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.5 44.9 - - + +
110A ALA* 3.7 7.4 - - + -
111A LYS* 3.6 26.8 - - + +
144A GLY 3.0 19.1 + - - +
145A PHE 3.7 4.0 - - - +
147A ASP* 1.3 74.6 - - - +
149A LEU* 1.3 65.5 + - - +
151A LYS* 3.2 22.6 + - - +
152A ASP* 2.9 57.0 + - - +
289A PGE 3.8 11.8 - - - -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 4.1 13.0 - - + +
114A LEU* 4.3 22.2 - - + -
118A TRP* 4.2 18.8 - - + -
145A PHE* 3.1 36.3 + - + +
146A LYS 3.3 7.2 + - - +
148A GLN* 1.3 76.3 - - - +
150A THR* 1.3 60.5 + - - +
152A ASP* 3.3 4.9 + - - +
153A GLY 3.1 4.3 + - - -
154A HIS* 2.9 42.0 + - + +
155A PRO* 4.2 4.5 - - + -
157A LEU* 4.0 25.8 - - + -
158A MET* 3.7 22.7 - - + +
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Residues in contact with THR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 2.9 31.4 + - - +
147A ASP* 3.6 9.2 - - - -
149A LEU* 1.3 75.1 - - - +
151A LYS* 1.3 60.9 + - - +
153A GLY* 2.9 20.3 + - - -
155A PRO* 3.7 29.3 - - + +
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LYS* 5.7 2.4 - - - +
147A ASP 2.9 17.4 + - - +
148A GLN* 3.5 25.4 - - - +
150A THR* 1.3 76.9 - - - +
152A ASP* 1.3 74.2 + - - +
153A GLY* 3.2 1.2 + - - -
289A PGE 6.6 0.4 - - - -
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA 5.4 0.3 - - - +
111A LYS* 4.3 15.4 + - - +
114A LEU* 3.6 29.8 - - + +
148A GLN* 2.9 47.6 + - - +
149A LEU* 4.0 3.5 - - - +
150A THR 3.2 0.2 - - - -
151A LYS* 1.3 89.4 + - - +
153A GLY* 1.3 58.4 + - - +
154A HIS* 3.3 14.8 + - - -
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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