Contacts of the helix formed by residues 142 - 157 (chain A) in PDB entry 2FN9
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.1 22.8 + - + +
140A LEU 3.3 0.2 - - - -
141A SER* 1.3 79.3 + - - +
143A GLN* 1.3 66.7 + - - +
144A PRO* 4.0 10.5 - - + -
145A THR* 3.2 23.3 + - - +
146A TRP* 3.6 8.5 - - - -
172A PHE* 4.3 11.7 - - + -
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Residues in contact with GLN 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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141A SER 3.8 2.8 + - - -
142A ALA* 1.3 70.9 - - - +
144A PRO* 1.4 72.4 - - + +
146A TRP* 3.0 16.5 + - - +
147A ASP* 2.9 54.1 + - - +
150A ASN* 5.9 1.0 - - - +
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Residues in contact with PRO 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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106A ASN* 3.6 32.1 - - - +
142A ALA* 3.5 9.9 - - + -
143A GLN* 1.4 93.7 - - + +
145A THR* 1.3 62.4 + - - +
147A ASP* 4.4 2.7 - - + -
148A ARG* 3.0 41.4 + - - +
172A PHE* 4.4 11.2 - - + -
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Residues in contact with THR 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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137A LEU* 4.2 11.1 - - + +
138A GLY 3.2 25.7 + - - +
139A ILE 2.7 36.0 + - - +
140A LEU* 4.7 0.9 - - - -
142A ALA* 3.2 12.9 + - - +
143A GLN 3.2 0.6 - - - -
144A PRO* 1.3 78.7 - - - +
146A TRP* 1.3 79.9 + - + +
148A ARG* 3.9 3.0 - - - +
149A SER* 3.1 26.3 + - - -
172A PHE* 3.3 17.8 - - - -
197A GLY* 6.0 1.9 - - - -
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Residues in contact with TRP 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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137A LEU* 3.9 26.7 - - + -
140A LEU* 2.8 51.9 + - + -
141A SER 5.3 0.2 - - - -
142A ALA 3.6 12.8 - - - -
143A GLN* 3.0 16.6 + - - +
145A THR* 1.3 85.6 - - + +
147A ASP* 1.3 62.1 + - - +
148A ARG 3.3 0.2 - - - -
149A SER* 4.3 11.2 - - - -
150A ASN* 2.7 61.0 + - - +
167A GLN* 4.9 9.6 - - - -
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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 TYR* 5.2 10.9 - - - -
106A ASN* 3.6 24.9 + - + +
107A TYR* 3.3 35.6 + - - +
143A GLN* 2.9 48.3 + - - +
144A PRO* 4.1 0.8 - - + +
146A TRP* 1.3 77.3 - - - +
148A ARG* 1.3 61.8 + - - +
150A ASN* 4.7 2.6 + - - -
151A GLY* 3.0 18.7 + - - -
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Residues in contact with ARG 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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106A ASN* 2.8 39.8 + - + +
110A GLY* 3.5 8.5 - - - -
144A PRO* 3.0 29.4 + - - +
145A THR* 3.9 3.1 - - - +
147A ASP* 1.3 77.7 - - - +
149A SER* 1.3 62.1 + - - +
152A PHE* 3.0 22.5 + - - +
172A PHE* 4.4 7.2 - - - -
195A TRP* 3.7 14.2 - - + -
197A GLY* 2.8 39.9 + - - +
198A ASN* 3.6 9.7 - - - +
222A PHE* 3.2 34.1 - - + -
223A ASP* 2.9 28.1 + - - -
244A GLN* 3.2 17.8 + - - +
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Residues in contact with SER 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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135A GLU* 2.7 34.8 + - - -
137A LEU* 3.6 15.3 - - - +
145A THR 3.1 19.6 + - - -
146A TRP* 4.0 13.6 - - - -
148A ARG* 1.3 75.2 - - - +
150A ASN* 1.3 59.7 + - - +
152A PHE* 3.3 2.4 + - - +
153A HIS* 2.9 40.1 + - - -
167A GLN* 4.2 2.9 + - - -
195A TRP* 4.4 4.9 - - - +
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Residues in contact with ASN 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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107A TYR* 3.8 18.1 + - + -
143A GLN* 5.9 0.8 - - - +
146A TRP* 2.7 50.7 + - - +
147A ASP* 5.1 2.2 + - - +
149A SER* 1.3 74.6 + - - +
151A GLY* 1.3 57.3 + - - +
153A HIS* 3.8 6.7 - - - +
154A SER* 2.9 30.5 + - - -
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Residues in contact with GLY 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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107A TYR* 3.6 37.3 - - - -
110A GLY 3.4 7.2 - - - -
111A VAL* 3.5 11.1 - - - -
147A ASP 3.0 14.6 + - - -
148A ARG 3.9 0.4 - - - -
150A ASN* 1.3 78.7 - - - +
152A PHE* 1.3 60.2 + - - +
154A SER* 2.7 20.4 + - - -
155A VAL 3.7 1.4 + - - -
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Residues in contact with PHE 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 GLY 3.1 14.8 + - - +
113A ALA 4.1 1.6 - - - -
114A GLY* 3.6 15.9 - - - -
117A PHE* 3.7 40.2 - + + -
133A TYR* 3.8 23.3 - + - -
148A ARG 3.0 15.3 + - - +
149A SER 3.5 7.2 - - - +
151A GLY* 1.3 74.9 - - - +
153A HIS* 1.3 73.2 + + - +
155A VAL* 3.1 6.6 + - - +
156A VAL* 3.0 48.3 + - + +
195A TRP* 3.4 62.8 - + + +
220A PHE* 5.8 0.2 - - + -
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Residues in contact with HIS 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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133A TYR* 3.2 24.2 + + - -
135A GLU* 2.7 23.2 + - - -
149A SER* 2.9 40.4 + - - +
150A ASN* 4.0 6.1 - - - +
152A PHE* 1.3 82.3 - + - +
154A SER* 1.3 65.8 + - - +
155A VAL 3.0 2.2 - - - -
156A VAL* 4.2 1.3 - - - +
157A ASP* 2.8 61.6 + - - +
164A MET* 3.6 24.1 - - + -
167A GLN* 4.1 3.9 + - - -
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Residues in contact with SER 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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107A TYR* 3.4 24.7 + - - -
111A VAL* 3.7 12.3 - - - +
150A ASN 2.9 11.1 + - - -
151A GLY 2.7 17.7 + - - -
153A HIS* 1.3 75.8 - - - +
155A VAL* 1.3 53.9 + - - +
157A ASP* 5.4 0.4 - - - +
158A GLN* 2.8 33.3 + - - +
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Residues in contact with VAL 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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111A VAL* 3.7 37.9 - - + +
114A GLY 3.7 24.9 - - - +
115A GLU* 3.7 15.3 - - + +
118A VAL* 4.4 1.8 - - + -
151A GLY 4.0 3.4 - - - +
152A PHE 3.1 6.3 + - - +
153A HIS 3.0 0.4 - - - -
154A SER* 1.3 82.6 + - - +
156A VAL* 1.3 67.4 + - - +
157A ASP 3.3 1.8 - - - -
158A GLN* 3.1 27.9 + - - +
159A TYR* 3.4 20.6 - - + +
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Residues in contact with VAL 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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114A GLY* 3.8 24.0 - - - +
117A PHE* 3.9 10.1 - - + -
118A VAL* 4.0 8.3 - - + -
133A TYR* 3.8 22.2 - - + +
152A PHE* 3.0 42.3 + - + +
155A VAL* 1.3 74.9 - - - +
157A ASP* 1.3 58.8 + - - +
158A GLN 3.0 0.2 - - - -
159A TYR* 2.9 28.6 + - - +
162A PHE* 3.7 31.5 - - + +
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Residues in contact with ASP 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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133A TYR* 4.2 4.5 + - - -
153A HIS* 2.8 56.8 + - - +
154A SER 5.4 0.2 - - - -
156A VAL* 1.3 77.6 - - - +
158A GLN* 1.3 60.4 + - + +
159A TYR 3.2 4.7 + - - -
160A PRO* 4.6 3.6 - - - +
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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