Contacts of the helix formed by residues 141 - 163 (chain A) in PDB entry 2FD5
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 GLU 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLY* 3.9 3.3 + - - -
80A LYS* 5.2 1.2 + - - +
83A ARG* 2.9 34.7 + - - +
136A ALA* 3.7 9.0 - - + -
137A GLU* 2.8 33.3 + - - +
138A SER* 2.9 25.6 + - - +
140A GLU* 1.3 80.3 - - + +
142A THR* 1.3 57.6 + - - +
143A ASP 3.4 1.6 - - - -
144A VAL* 3.3 10.1 + - + +
145A ALA* 2.9 31.7 + - - +
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Residues in contact with THR 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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132A VAL* 3.7 20.6 - - + +
136A ALA* 3.8 12.5 - - - +
138A SER 3.7 2.5 + - - -
139A PRO* 3.2 24.6 + - - +
141A GLU* 1.3 78.1 - - - +
143A ASP* 1.3 65.2 + - - +
145A ALA* 3.3 2.9 + - - +
146A LEU* 3.0 32.1 + - + +
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A PRO 4.7 0.6 + - - -
140A GLU 4.3 6.9 + - - +
141A GLU 3.4 0.2 - - - -
142A THR* 1.3 82.3 - - - +
144A VAL* 1.3 61.8 + - + +
146A LEU* 3.6 14.5 - - - +
147A ALA* 3.0 30.7 + - - +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.9 9.0 - - - +
140A GLU 4.1 15.3 - - - +
141A GLU* 3.3 13.8 + - + +
143A ASP* 1.3 78.3 - - + +
145A ALA* 1.3 58.6 + - - +
147A ALA* 3.4 5.6 + - - +
148A ASP* 2.9 34.9 + - - +
180A ASN* 3.4 48.2 - - + +
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Residues in contact with ALA 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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83A ARG* 3.9 14.8 - - - +
132A VAL* 4.1 21.1 - - + +
135A LEU* 4.0 30.9 - - + +
136A ALA* 4.4 0.7 - - + -
141A GLU 2.9 16.3 + - - +
142A THR 3.7 4.3 - - - +
144A VAL* 1.3 76.4 - - - +
146A LEU* 1.3 57.7 + - - +
148A ASP* 3.2 3.8 + - - +
149A LEU* 3.0 31.7 + - - +
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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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128A VAL* 3.8 21.5 - - + -
132A VAL* 3.6 24.1 - - + +
142A THR* 3.0 21.7 + - + +
143A ASP* 3.6 16.2 - - - +
144A VAL 3.3 0.2 - - - -
145A ALA* 1.3 76.1 - - - +
147A ALA* 1.3 63.1 + - - +
149A LEU* 3.2 9.9 + - + +
150A VAL* 3.1 30.1 + - + +
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Residues in contact with ALA 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 ASP 3.0 17.7 + - - +
144A VAL* 3.8 5.6 - - - +
146A LEU* 1.3 76.0 - - - +
148A ASP* 1.3 59.6 + - - +
150A VAL* 3.2 11.7 + - - +
151A LEU* 2.9 34.9 + - + +
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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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83A ARG* 3.2 18.0 + - + -
135A LEU* 6.1 0.7 - - + -
144A VAL* 2.9 22.5 + - - +
145A ALA* 3.5 7.4 - - - +
146A LEU 3.2 0.4 - - - -
147A ALA* 1.3 77.3 - - - +
149A LEU* 1.3 65.2 + - - +
151A LEU* 3.2 12.2 + - - +
152A MET* 3.0 41.5 + - + +
178A ALA 4.5 0.2 - - - +
179A VAL* 3.4 22.7 - - + +
180A ASN* 2.6 42.4 + - - +
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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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90A TYR* 6.3 2.5 - - + -
127A HIS* 6.4 0.4 - - + -
128A VAL* 4.5 15.0 - - + +
131A MET* 4.0 35.7 - - + -
132A VAL* 3.6 31.9 - - + +
135A LEU* 4.6 10.5 - - + -
145A ALA 3.0 13.0 + - - +
146A LEU* 3.2 9.8 + - + +
148A ASP* 1.3 75.6 - - - +
150A VAL* 1.3 58.4 + - + +
152A MET* 3.3 21.3 + - + +
153A ILE* 2.9 49.3 + - + +
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Residues in contact with VAL 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 20.8 + - + +
147A ALA* 3.4 11.0 - - - +
149A LEU* 1.3 77.7 - - + +
151A LEU* 1.3 60.2 + - + +
153A ILE* 5.0 4.5 - - + -
154A GLY* 2.9 32.4 + - - +
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Residues in contact with LEU 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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91A LEU* 3.9 2.5 - - - +
147A ALA* 2.9 22.2 + - + +
148A ASP* 3.2 12.3 + - - +
150A VAL* 1.3 77.1 - - + +
152A MET* 1.3 57.9 + - - +
155A GLY* 2.9 28.2 + - - +
175A ALA* 3.7 36.5 - - + +
178A ALA* 3.7 41.3 - - + +
179A VAL* 3.9 14.4 - - + +
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Residues in contact with MET 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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83A ARG* 4.4 6.1 - - - +
86A ALA* 4.0 17.5 - - + +
87A ALA* 4.0 30.7 - - + +
90A TYR* 3.1 54.7 - - + -
91A LEU* 3.5 11.4 - - + +
135A LEU* 4.8 7.9 - - + -
148A ASP* 3.0 37.2 + - + +
149A LEU* 3.6 25.4 - - + +
151A LEU* 1.3 74.9 - - + +
153A ILE* 1.3 67.8 + - + +
156A LEU 3.0 18.5 + - - -
179A VAL* 5.3 0.4 - - + -
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Residues in contact with ILE 153 (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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90A TYR* 3.7 22.2 - - + +
106A LEU* 3.7 38.4 - - + -
107A PRO* 3.8 16.0 - - + +
110A LEU* 3.8 29.8 - - + -
128A VAL* 5.9 5.4 - - + -
149A LEU* 2.9 39.0 + - + +
150A VAL* 4.4 3.6 - - + +
152A MET* 1.3 74.4 - - + +
154A GLY* 1.3 58.8 + - - +
156A LEU 3.4 0.2 + - - -
157A ALA* 3.0 28.6 + - + +
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Residues in contact with GLY 154 (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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150A VAL* 2.9 18.4 + - - +
153A ILE* 1.3 77.2 - - - +
155A GLY* 1.3 58.0 + - - +
157A ALA* 3.3 6.8 + - - +
158A LEU* 2.9 32.4 + - - +
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Residues in contact with GLY 155 (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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91A LEU* 3.9 10.8 - - - -
151A LEU* 2.9 22.8 + - - +
154A GLY* 1.3 76.4 - - - +
156A LEU* 1.3 58.1 + - - +
158A LEU* 4.9 0.2 - - - -
159A ALA* 2.9 31.6 + - - +
171A VAL* 3.5 12.4 - - - +
172A LEU* 4.2 0.6 - - - +
175A ALA* 4.2 11.7 - - - -
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Residues in contact with LEU 156 (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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90A TYR* 3.6 29.4 - - + +
91A LEU* 3.6 3.1 - - - +
92A SER 4.0 1.6 - - - +
95A HIS* 3.6 28.3 - - + +
96A ARG* 3.6 27.8 - - + +
104A CYS 5.5 0.2 - - - +
107A PRO* 3.9 12.1 - - + -
152A MET 3.0 18.3 + - - +
153A ILE 3.9 2.2 - - - +
155A GLY* 1.3 73.7 - - - +
157A ALA* 1.3 60.2 + - - +
159A ALA* 3.9 0.3 - - - +
160A ARG* 2.9 59.3 + - - +
172A LEU* 3.9 19.7 - - + -
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Residues in contact with ALA 157 (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 PRO* 4.1 26.7 - - + +
153A ILE* 3.0 19.5 + - + +
154A GLY* 3.6 8.5 - - - +
156A LEU* 1.3 77.2 - - - +
158A LEU* 1.3 63.2 + - - +
160A ARG* 3.7 4.4 - - - +
161A ALA* 3.1 24.0 + - - +
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Residues in contact with LEU 158 (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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154A GLY 2.9 17.5 + - - +
155A GLY* 4.0 2.9 - - - +
157A ALA* 1.3 74.3 - - - +
159A ALA* 1.3 65.4 + - - +
161A ALA* 3.3 9.0 + - + +
162A LEU* 3.0 46.9 + - + +
171A VAL* 3.9 25.4 - - + -
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Residues in contact with ALA 159 (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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96A ARG* 3.6 8.0 - - + -
155A GLY 2.9 19.4 + - - +
156A LEU 3.9 2.5 - - - +
158A LEU* 1.3 76.6 - - - +
160A ARG* 1.3 62.6 + - - +
162A LEU* 3.3 2.2 + - - -
163A GLY 3.2 12.8 + - - -
168A SER* 2.6 38.1 + - - +
171A VAL* 3.9 7.5 - - + +
172A LEU* 3.6 29.8 - - + -
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Residues in contact with ARG 160 (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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21A LEU 3.8 20.7 + - - -
22A GLU* 5.6 6.6 + - - +
95A HIS* 3.1 29.3 + - - -
96A ARG* 2.9 31.4 + - + +
98A ALA* 4.8 8.1 - - - +
104A CYS 5.0 4.8 + - - -
107A PRO* 3.7 25.6 - - - +
108A ALA* 4.5 5.5 - - - +
156A LEU* 2.9 37.5 + - - +
157A ALA* 3.7 4.7 - - - +
159A ALA* 1.3 73.5 - - - +
161A ALA* 1.3 67.7 + - - +
163A GLY* 3.1 14.1 + - - -
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Residues in contact with ALA 161 (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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157A ALA 3.1 19.0 + - - +
158A LEU* 3.5 13.2 - - + +
160A ARG* 1.3 76.7 - - - +
162A LEU* 1.3 62.9 + - + +
163A GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 162 (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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158A LEU* 3.0 36.7 + - + +
159A ALA 3.8 4.9 - - - +
160A ARG 3.2 0.2 - - - -
161A ALA* 1.3 77.9 - - + +
163A GLY* 1.3 63.3 + - - +
164A PRO 4.7 1.2 - - - +
167A LEU* 3.9 32.3 - - + -
168A SER* 4.1 13.0 - - - +
171A VAL* 3.7 29.8 - - + -
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Residues in contact with GLY 163 (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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96A ARG* 4.9 1.6 - - - -
159A ALA 3.2 4.7 + - - -
160A ARG* 3.1 17.7 + - - -
161A ALA 3.2 0.6 - - - -
162A LEU* 1.3 80.8 - - - +
164A PRO* 1.3 80.4 - - - +
165A GLY* 4.3 0.5 - - - -
168A SER* 3.0 21.7 - - - -
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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
------------------------------------------------------------
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