Contacts of the helix formed by residues 131 - 152 (chain A) in PDB entry 2R5G
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 ALA 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASN* 3.8 7.2 - - - +
128A GLN* 2.9 19.4 + - + +
130A GLU* 1.3 75.2 - - - +
132A ASN* 1.3 63.7 + - - +
133A LYS 3.3 2.7 - - - -
134A ASN* 3.2 21.4 + - + +
135A PHE* 3.2 34.6 + - + -
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 4.9 5.4 + - + -
126A ASN* 2.9 13.5 + - - +
128A GLN 3.6 1.2 + - - -
129A LYS* 3.1 29.9 + - + +
130A GLU 3.3 0.4 - - - -
131A ALA* 1.3 77.6 - - - +
133A LYS* 1.3 58.7 + - - +
135A PHE* 3.3 4.3 + - - +
136A GLU* 2.8 34.2 + - + +
201A ARG* 4.3 16.3 - - - +
245A GLN* 2.7 44.0 - - - +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS 4.9 0.2 + - - -
130A GLU 4.7 5.8 + - - +
131A ALA 3.3 1.0 - - - -
132A ASN* 1.3 77.7 - - - +
134A ASN* 1.3 62.2 + - - +
136A GLU* 3.3 29.4 + - - +
137A LYS* 2.9 65.6 + - + +
140A LEU* 6.1 2.0 - - - +
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Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA* 3.2 14.0 + - + +
133A LYS* 1.3 81.4 - - - +
135A PHE* 1.3 64.7 + - + +
137A LYS* 3.4 13.8 + - - +
138A SER* 2.9 29.4 + - - -
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS 4.9 1.5 - - - +
122A ALA* 3.8 38.6 - - + -
123A TYR* 3.7 26.5 - - + +
126A ASN* 3.4 37.9 - - + +
131A ALA* 3.2 31.6 + - + -
132A ASN* 3.9 6.3 - - - +
134A ASN* 1.3 82.0 - - + +
136A GLU* 1.3 57.5 + - - +
138A SER* 3.3 10.0 + - - -
139A LEU* 3.0 27.5 + - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.7 19.6 + - + -
132A ASN 2.8 18.3 + - - +
133A LYS* 3.3 31.5 + - - +
135A PHE* 1.3 74.1 - - - +
137A LYS* 1.3 60.6 + - - +
139A LEU* 3.2 3.7 + - - +
140A LEU* 2.9 43.3 + - + +
201A ARG 5.3 3.1 - - - +
203A PHE* 3.9 25.8 - - + +
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 2.9 54.2 + - + +
134A ASN* 3.6 12.3 + - - +
136A GLU* 1.3 74.5 - - - +
138A SER* 1.3 57.7 + - - +
140A LEU* 3.4 13.2 + - + +
141A LYS* 2.9 33.0 + - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.6 35.4 + - - +
134A ASN 2.9 14.9 + - - -
135A PHE* 3.4 15.9 - - - -
137A LYS* 1.3 76.4 - - - +
139A LEU* 1.3 62.3 + - - +
141A LYS* 3.3 8.0 + - - +
142A GLU* 3.2 21.7 + - - +
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Residues in contact with LEU 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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116A LEU* 3.8 13.7 - - + +
119A LYS* 4.2 10.0 - - + +
120A PHE* 4.0 31.6 - - + +
123A TYR* 3.6 37.9 - - + -
135A PHE 3.0 14.2 + - - +
136A GLU* 3.2 8.9 + - - +
138A SER* 1.3 74.8 - - - +
140A LEU* 1.3 58.4 + - - +
142A GLU* 3.2 2.9 + - - -
143A PHE* 2.9 49.6 + - + -
193A ILE* 4.6 2.2 - - + -
203A PHE* 4.1 22.7 - - + -
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Residues in contact with LEU 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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133A LYS* 6.1 2.0 - - - +
136A GLU* 2.9 36.1 + - + +
137A LYS* 3.6 12.1 - - + +
139A LEU* 1.3 76.6 - - - +
141A LYS* 1.3 57.6 + - - +
143A PHE* 3.3 6.3 + - + +
144A LYS* 2.9 28.2 + - - +
203A PHE* 3.9 18.4 - - + -
206A PRO* 3.5 37.7 - - + -
209A PHE* 3.7 13.7 - - + -
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Residues in contact with LYS 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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119A LYS* 6.3 0.4 - - - +
137A LYS 2.9 17.9 + - - +
138A SER* 3.6 8.7 - - - +
139A LEU 3.2 0.2 - - - -
140A LEU* 1.3 75.0 - - - +
142A GLU* 1.3 60.6 + - - +
144A LYS* 3.2 14.0 + - + +
145A ARG* 3.0 32.3 + - + +
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Residues in contact with GLU 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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112A VAL* 4.9 6.5 - - + +
115A ASN* 3.3 29.9 + - - +
116A LEU* 3.5 39.1 - - + +
119A LYS* 3.3 29.6 + - + -
138A SER 3.2 11.9 + - - +
139A LEU 3.7 6.7 - - - +
141A LYS* 1.3 77.6 - - - +
143A PHE* 1.3 65.0 + - - +
145A ARG* 3.1 32.8 + - - +
146A LEU* 3.0 21.0 + - - +
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Residues in contact with PHE 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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116A LEU* 3.6 16.5 - - + +
139A LEU* 2.9 47.3 + - + +
140A LEU* 3.3 8.0 + - - +
142A GLU* 1.3 74.6 - - - +
144A LYS* 1.3 57.6 + - - +
146A LEU* 3.2 5.4 + - + +
147A ASP* 2.8 29.5 + - - +
190A LEU* 3.7 24.5 - - + -
193A ILE* 3.8 18.8 - - + -
203A PHE* 3.9 26.2 - + - -
205A ILE* 3.7 32.1 - - + -
209A PHE* 3.6 18.8 - + + -
212A VAL* 3.8 22.2 - - + +
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Residues in contact with LYS 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 LEU 2.9 13.5 + - - +
141A LYS* 3.2 18.6 + - + +
143A PHE* 1.3 74.7 - - - +
145A ARG* 1.3 59.0 + - - +
147A ASP* 3.4 8.1 - - - +
148A ASP* 2.8 61.7 + - - +
209A PHE* 3.5 30.2 - - + -
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Residues in contact with ARG 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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112A VAL* 4.3 8.6 - - + +
141A LYS* 3.0 23.6 + - + +
142A GLU* 3.1 35.4 + - - +
144A LYS* 1.3 77.0 - - - +
146A LEU* 1.3 57.3 + - - +
148A ASP* 3.3 9.0 + - - +
149A TYR* 2.9 28.6 + - - +
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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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112A VAL* 3.6 29.3 - - + +
116A LEU* 3.8 27.8 - - + -
142A GLU 3.0 12.0 + - - +
143A PHE* 3.2 10.7 + - + +
145A ARG* 1.3 72.9 - - - +
147A ASP* 1.3 66.5 - - - +
149A TYR* 3.1 4.5 + - + +
150A LEU* 2.9 37.0 + - + +
174A LEU* 3.9 26.9 - - + -
186A LEU* 4.0 12.3 - - + -
190A LEU* 4.2 17.3 - - + -
212A VAL* 4.0 14.8 - - + -
215A TYR* 5.2 0.2 - - + -
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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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143A PHE 2.8 20.3 + - - +
144A LYS* 3.4 15.6 - - + +
146A LEU* 1.3 72.3 - - - +
148A ASP* 1.3 57.5 + - - +
150A LEU* 3.3 2.8 + - - +
151A ASN* 2.9 46.7 + - - +
208A GLU 4.2 2.6 - - - +
209A PHE* 3.0 38.9 - - + -
210A SER* 4.1 1.2 + - - -
211A GLY 2.8 27.4 + - - -
212A VAL* 3.1 15.7 + - + +
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Residues in contact with ASP 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 LYS* 2.8 52.6 + - - +
145A ARG* 3.6 7.4 - - - +
147A ASP* 1.3 72.2 - - - +
149A TYR* 1.3 58.0 + - - +
151A ASN* 3.2 5.8 + - - +
152A THR* 2.8 40.5 + - - +
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Residues in contact with TYR 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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106A TYR* 4.0 5.0 - - - +
108A GLU* 3.7 22.9 - - + +
109A SER* 2.7 41.7 + - - -
112A VAL* 4.2 14.8 - - + -
145A ARG 2.9 13.6 + - - +
146A LEU* 3.1 11.0 + - - +
148A ASP* 1.3 76.6 - - - +
150A LEU* 1.3 61.4 + - + +
152A THR* 3.3 12.9 - - - +
154A LEU* 3.7 23.3 - - + +
171A ARG* 2.9 42.8 + - - -
174A LEU* 3.4 27.4 - - + -
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Residues in contact with LEU 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* 2.9 34.1 + - + +
147A ASP 3.8 4.0 - - - +
149A TYR* 1.3 76.5 - - + +
151A ASN* 1.3 59.4 + - - +
169A SER* 3.4 10.6 - - - -
171A ARG* 3.5 8.0 + - - +
172A LEU 5.4 0.2 - - - +
173A PHE* 4.2 17.7 - - - +
174A LEU* 4.1 21.5 - - + -
211A GLY* 3.4 31.9 - - - +
212A VAL* 3.8 8.1 - - - -
214A ARG* 2.9 31.6 + - - +
215A TYR* 3.5 35.0 - - + -
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Residues in contact with ASN 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 ASP* 2.9 37.1 + - - +
148A ASP* 4.0 5.3 + - - +
150A LEU* 1.3 75.8 - - - +
152A THR* 1.3 59.6 + - - +
153A PRO* 3.7 0.3 - - - +
167A PRO 4.8 0.3 - - - +
168A VAL* 3.3 22.2 - - + +
169A SER* 2.8 29.0 + - - +
210A SER* 3.8 11.2 + - - -
211A GLY* 3.3 16.0 + - - +
214A ARG* 3.2 21.7 + - - -
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Residues in contact with THR 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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148A ASP* 2.8 25.6 + - - +
149A TYR* 3.3 8.1 + - - +
150A LEU 3.4 0.2 - - - -
151A ASN* 1.3 77.7 - - - +
153A PRO* 1.3 81.8 - - + +
154A LEU* 3.4 2.4 + - - +
169A SER* 3.7 1.1 - - - -
171A ARG* 2.9 17.7 + - - -
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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
------------------------------------------------------------
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