Contacts of the helix formed by residues 137 - 151 (chain A) in PDB entry 4RG1
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 GLN 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 6.1 0.4 - - - +
93A ARG* 4.4 7.2 - - - +
136A GLY* 1.3 71.4 - - - -
138A ALA* 1.3 57.4 + - - +
140A VAL* 3.4 5.0 + - - +
141A GLN* 3.0 30.3 + - - +
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Residues in contact with ALA 138 (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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81A GLY 3.3 25.6 - - - +
82A SER* 4.4 0.7 - - - +
84A LEU* 3.9 7.0 - - + +
85A ASP* 3.6 31.2 + - - +
93A ARG* 3.6 15.4 - - - +
136A GLY 3.4 1.7 - - - +
137A GLN* 1.3 75.0 - - - +
139A CYS* 1.3 61.7 + - - +
141A GLN* 3.8 1.3 - - - +
142A LEU* 2.8 32.1 + - - +
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Residues in contact with CYS 139 (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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81A GLY* 3.6 15.7 - - - -
82A SER 4.6 1.1 - - - -
114A VAL* 3.8 15.6 - - + +
115A PHE 3.5 32.5 - - - -
116A ASP* 3.9 10.8 - - - -
136A GLY* 3.4 25.0 + - - +
137A GLN 3.3 0.4 - - - -
138A ALA* 1.3 78.6 - - - +
140A VAL* 1.3 58.4 + - + +
142A LEU* 3.5 1.7 + - - +
143A ALA* 3.0 30.5 + - - +
266A LEU* 3.8 14.2 - - + +
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Residues in contact with VAL 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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136A GLY 3.1 19.2 + - - +
137A GLN* 3.9 5.6 - - - +
139A CYS* 1.3 79.4 - - + +
141A GLN* 1.3 64.1 + - - +
143A ALA* 3.4 5.6 + - - +
144A ARG* 3.0 30.7 + - + +
266A LEU* 4.7 17.3 - - + -
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Residues in contact with GLN 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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84A LEU* 4.0 7.1 - - + +
90A PRO 5.4 0.2 + - - -
93A ARG* 2.5 56.3 + - - +
94A THR* 4.4 10.1 + - - +
137A GLN 3.0 17.6 + - - +
138A ALA 3.8 3.4 - - - +
140A VAL* 1.3 75.5 - - - +
142A LEU* 1.3 64.9 + - - +
144A ARG* 3.4 5.6 + - - +
145A ILE* 3.2 44.8 + - + +
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Residues in contact with LEU 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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79A LEU* 4.5 17.0 - - + -
80A PRO 4.4 5.8 - - - +
81A GLY* 4.0 14.8 - - - +
83A ILE* 4.9 4.3 - - + -
84A LEU* 3.8 19.2 - - + +
97A ALA* 3.8 30.1 - - + +
100A ILE* 4.6 7.9 - - + -
114A VAL* 3.9 25.1 - - + -
138A ALA 2.8 22.7 + - - +
139A CYS 3.7 3.6 - - - +
141A GLN* 1.3 73.2 - - - +
143A ALA* 1.3 63.1 + - - +
145A ILE* 3.2 4.5 + - - +
146A LEU* 2.9 45.8 + - + +
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Residues in contact with ALA 143 (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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114A VAL* 4.4 4.0 - - + +
139A CYS 3.0 18.5 + - - +
140A VAL 3.8 3.1 - - - +
142A LEU* 1.3 75.5 - - - +
144A ARG* 1.3 57.0 + - - +
146A LEU* 3.3 6.7 + - - +
147A GLN* 2.9 38.0 + - - +
264A VAL* 3.7 25.3 - - + +
266A LEU* 4.0 25.4 - - + -
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Residues in contact with ARG 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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140A VAL* 3.0 24.8 + - + +
141A GLN* 3.9 6.1 - - - +
142A LEU 3.2 0.2 - - - -
143A ALA* 1.3 74.0 - - - +
145A ILE* 1.3 66.1 + - + +
147A GLN* 3.4 11.7 + - - +
148A TYR* 3.0 24.1 + - - +
160A PHE* 4.4 12.6 - - + -
166A LEU* 4.5 23.1 - - + -
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Residues in contact with ILE 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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84A LEU* 5.0 0.7 - - + -
94A THR* 4.4 18.2 - - + +
97A ALA* 3.5 34.5 - - + -
98A GLY 4.5 0.4 - - - +
141A GLN* 3.2 43.0 + - + +
142A LEU 3.7 3.4 - - - +
144A ARG* 1.3 76.7 - - + +
146A LEU* 1.3 64.1 - - - +
148A TYR* 3.3 1.8 + - + +
149A LEU* 3.0 42.1 + - + +
166A LEU* 4.1 20.9 - - + -
169A ALA* 3.9 17.5 - - + -
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Residues in contact with LEU 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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97A ALA 3.7 15.5 - - - +
100A ILE* 4.2 9.4 - - + -
101A ALA* 3.6 34.5 - - + +
112A ILE* 3.7 34.3 - - + -
114A VAL* 3.9 19.1 - - + -
142A LEU* 2.9 28.3 + - + +
143A ALA* 3.5 8.5 - - - +
145A ILE* 1.3 77.3 - - - +
147A GLN* 1.3 61.4 + - - +
149A LEU 3.5 0.2 + - - -
150A GLU 3.1 10.0 + - - -
262A TYR* 2.8 29.3 + - + +
264A VAL* 3.8 11.7 - - + -
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Residues in contact with GLN 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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143A ALA* 2.9 23.4 + - - +
144A ARG* 3.8 13.2 - - - +
146A LEU* 1.3 73.4 - - - +
148A TYR* 1.3 65.2 + - - +
150A GLU* 3.2 7.7 + - - +
151A CYS* 3.1 23.0 + - - +
160A PHE* 3.7 19.2 - - + -
264A VAL* 3.6 29.0 + - + +
402A 15P 3.2 46.9 + - - -
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Residues in contact with TYR 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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144A ARG 3.0 18.5 + - - +
145A ILE 3.6 3.8 - - - +
147A GLN* 1.3 75.6 - - - +
149A LEU* 1.3 74.6 + - + +
151A CYS* 3.2 8.1 + - - +
156A ARG* 3.0 60.1 + - + +
160A PHE* 3.7 32.5 - + + -
162A LYS* 4.3 16.7 - - + +
166A LEU* 3.1 55.9 - - + -
167A GLN* 3.4 19.2 + - - +
169A ALA* 5.1 1.6 - - + -
170A GLY* 4.2 13.2 - - - -
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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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98A GLY* 3.8 20.6 - - - -
101A ALA* 3.6 23.8 - - + -
145A ILE* 3.0 32.4 + - + +
146A LEU 3.9 3.4 - - - +
148A TYR* 1.3 81.5 - - + +
150A GLU* 1.3 62.0 + - - +
156A ARG* 3.3 13.0 + - - +
169A ALA* 3.8 5.6 - - + +
170A GLY* 3.5 32.1 - - - +
173A ASN 3.4 22.7 - - - +
174A PRO* 4.8 3.1 - - + -
175A LEU* 3.5 17.5 + - + +
180A HIS* 3.2 18.4 - - - -
262A TYR* 4.1 2.7 - - - +
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Residues in contact with GLU 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 LEU 3.1 17.9 + - - +
147A GLN* 3.7 7.8 - - - +
148A TYR 3.2 0.2 - - - -
149A LEU* 1.3 75.8 - - - +
151A CYS* 1.3 58.2 + - - +
152A PRO 3.3 0.2 - - - -
175A LEU* 3.8 9.9 - - + -
179A HIS* 2.8 27.7 + - + +
180A HIS* 2.7 21.8 + - - -
226A ARG* 2.9 38.6 + - - -
260A TRP 4.0 2.6 - - - +
261A GLY* 3.9 6.9 - - - -
262A TYR* 3.3 49.8 + - + +
402A 15P 3.5 10.5 + - - +
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Residues in contact with CYS 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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147A GLN 3.1 12.2 + - - +
148A TYR 3.2 10.6 + - - +
150A GLU* 1.3 81.4 + - - +
152A PRO* 1.3 86.9 - - - +
155A LEU* 3.7 29.8 - - - -
156A ARG* 2.8 33.3 + - + -
159A PHE* 4.1 9.0 - - - -
160A PHE* 3.7 19.5 - - + -
180A HIS* 3.9 0.6 + - - -
226A ARG* 4.1 9.4 - - - +
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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
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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