Contacts of the helix formed by residues 137 - 151 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 4.5 6.5 - - - +
136B GLY* 1.3 74.7 - - - +
138B ALA* 1.3 59.6 + - - +
140B VAL* 3.5 5.0 + - - +
141B GLN* 3.0 30.8 + - - +
165B ASP* 5.1 0.9 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLY 3.2 25.8 - - - +
82B SER* 4.2 5.2 - - - +
84B LEU* 3.6 8.1 - - + +
85B ASP* 3.8 24.0 - - - +
93B ARG* 3.6 15.6 - - - +
136B GLY 3.4 1.2 - - - +
137B GLN* 1.3 78.3 - - - +
139B CYS* 1.3 58.7 + - - +
141B GLN* 3.5 0.6 + - - -
142B LEU* 2.9 31.7 + - - +
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Residues in contact with CYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY* 3.7 15.5 - - - -
82B SER 4.7 1.3 - - - -
114B VAL* 3.8 18.0 - - + +
115B PHE 3.6 31.4 - - - -
116B ASP* 4.0 17.9 - - - -
136B GLY* 3.4 13.1 + - - +
137B GLN 3.3 0.6 - - - -
138B ALA* 1.3 78.9 - - - +
140B VAL* 1.3 59.0 + - + +
142B LEU* 3.4 1.6 + - - +
143B ALA* 2.9 31.2 + - - +
266B LEU* 4.1 11.9 - - + -
267B ALA 5.7 0.2 - - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.1 18.3 + - - +
137B GLN* 4.0 5.4 - - - +
139B CYS* 1.3 77.5 - - + +
141B GLN* 1.3 58.0 + - - +
143B ALA* 3.4 1.9 + - - -
144B ARG* 2.9 57.1 + - - +
165B ASP* 4.3 2.9 - - - +
266B LEU* 4.7 13.0 - - + -
404B 15P 3.6 17.5 + - - +
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.0 9.1 - - + +
90B PRO 5.2 1.0 + - - -
93B ARG* 2.5 43.7 + - - +
94B THR* 3.8 16.2 + - - +
137B GLN 3.0 18.4 + - - +
138B ALA* 3.9 2.9 - - - +
140B VAL* 1.3 76.6 - - - +
142B LEU* 1.3 62.3 + - - +
144B ARG* 3.4 1.6 + - - +
145B ILE* 3.1 32.8 + - + +
164B GLN 5.4 0.4 + - - -
165B ASP* 3.5 53.1 + - + +
168B PHE* 6.0 1.0 - - - -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 4.4 23.6 - - + -
80B PRO 4.4 1.3 - - - +
81B GLY* 4.0 20.2 - - - +
83B ILE* 4.9 5.6 - - + -
84B LEU* 3.7 16.7 - - + +
97B ALA* 3.7 31.9 - - + +
100B ILE* 4.5 7.6 - - + -
114B VAL* 4.0 17.9 - - + -
138B ALA 2.9 18.9 + - - +
139B CYS 3.8 3.6 - - - +
141B GLN* 1.3 74.5 - - - +
143B ALA* 1.3 65.5 + - - +
145B ILE* 3.2 3.1 + - - +
146B LEU* 2.9 47.4 + - + +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 4.6 3.1 - - + -
139B CYS 2.9 17.9 + - - +
140B VAL 3.8 4.3 - - - +
142B LEU* 1.3 76.1 - - - +
144B ARG* 1.3 57.0 + - - +
146B LEU* 3.3 6.3 + - - +
147B GLN* 3.0 34.4 + - - +
264B VAL* 3.9 23.5 - - + +
266B LEU* 3.8 17.9 - - + -
404B 15P 3.8 17.5 - - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 2.9 40.8 + - - +
141B GLN* 3.8 4.9 - - - +
142B LEU 3.3 0.2 - - - -
143B ALA* 1.3 74.1 - - - +
145B ILE* 1.3 61.3 + - - +
147B GLN* 3.4 9.1 + - - +
148B TYR* 2.9 27.4 + - - +
160B PHE* 4.4 11.6 - - + -
163B HIS* 3.4 48.3 + - - +
165B ASP* 3.3 22.0 + - + -
166B LEU* 4.2 20.6 - - + -
404B 15P 4.0 11.0 + - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 5.2 0.2 - - + -
93B ARG 5.0 0.2 - - - +
94B THR* 4.1 23.3 - - + +
97B ALA* 3.6 33.0 - - + -
98B GLY 4.3 0.4 - - - +
141B GLN* 3.1 30.1 + - + +
142B LEU 3.8 3.1 - - - +
144B ARG* 1.3 71.5 - - - +
146B LEU* 1.3 67.4 + - - +
148B TYR* 3.2 1.4 + - - +
149B LEU* 3.0 32.6 + - + +
165B ASP 3.8 24.5 - - - +
166B LEU* 3.9 14.6 - - + -
172B LEU* 3.7 28.5 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 3.7 14.6 - - - +
100B ILE* 4.2 6.5 - - + -
101B ALA* 3.6 33.4 - - + +
112B ILE* 3.6 35.9 - - + -
114B VAL* 3.9 18.2 - - + -
142B LEU* 2.9 31.4 + - + +
143B ALA 3.6 6.5 - - - +
145B ILE* 1.3 77.5 - - - +
147B GLN* 1.3 61.4 + - - +
149B LEU 3.4 0.2 + - - -
150B GLU 3.1 10.7 + - - -
262B TYR* 2.7 28.8 + - + +
264B VAL* 3.8 14.1 - - + -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA 3.0 18.2 + - - +
144B ARG* 3.9 7.6 - - - +
146B LEU* 1.3 75.7 - - - +
148B TYR* 1.3 63.2 + - - +
150B GLU* 3.3 8.7 + - - +
151B CYS* 3.1 19.2 + - - +
160B PHE* 3.6 23.9 - - + -
264B VAL* 3.7 24.5 - - + +
404B 15P 3.3 80.9 + - - +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ARG 2.9 17.1 + - - +
145B ILE 3.2 3.1 + - - +
147B GLN* 1.3 79.3 - - - +
149B LEU* 1.3 77.8 + - + +
151B CYS* 3.3 6.1 + - - +
156B ARG* 3.1 63.2 + - + +
160B PHE* 3.8 31.3 - + + -
166B LEU* 3.7 34.3 - - + -
169B ALA* 3.9 29.3 - - + +
172B LEU* 4.6 3.1 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 3.8 20.4 - - - +
101B ALA* 3.7 23.1 - - + -
145B ILE* 3.0 21.3 + - + +
146B LEU 3.9 3.1 - - - +
148B TYR* 1.3 87.6 - - + +
150B GLU* 1.3 59.6 + - - +
156B ARG* 3.3 21.0 + - - +
172B LEU* 3.8 37.7 - - + -
173B ASN 4.0 16.6 - - - +
174B PRO* 4.7 9.0 - - + -
175B LEU* 3.6 17.7 + - + +
180B HIS* 3.3 12.1 - - - -
262B TYR* 4.2 2.9 - - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU 3.1 16.2 + - - +
147B GLN* 3.7 8.3 - - - +
148B TYR 3.3 0.2 - - - -
149B LEU* 1.3 75.4 - - - +
151B CYS* 1.3 60.2 + - - +
175B LEU* 3.9 9.9 - - + -
179B HIS* 2.8 27.0 + - + +
180B HIS* 2.7 23.0 + - - -
226B ARG* 2.9 37.9 + - - -
260B TRP 4.1 0.9 - - - +
261B GLY* 4.0 5.6 - - - -
262B TYR* 3.2 50.6 + - + +
404B 15P 3.6 14.1 + - - +
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Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN 3.1 7.0 + - - +
148B TYR 3.6 6.3 - - - +
149B LEU 3.3 0.6 - - - -
150B GLU* 1.3 80.7 - - - +
152B PRO* 1.3 85.8 - - - +
155B LEU* 3.7 29.4 - - - -
156B ARG* 3.0 29.5 + - + -
159B PHE* 4.2 9.2 - - - -
160B PHE* 3.6 31.4 - - + -
180B HIS* 3.9 1.0 + - - -
226B ARG* 4.4 9.0 - - - +
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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