Contacts of the helix formed by residues 150 - 159 (chain A) in PDB entry 3FHX
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 ASN 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY 3.0 22.1 + - - +
118A ASP* 3.4 25.9 - - - +
149A PRO* 1.3 76.6 - - - +
151A GLN* 1.3 65.8 + - - +
152A PHE* 3.2 5.1 + - - +
153A GLU* 2.8 41.5 + - - +
154A ALA* 3.0 15.4 + - - +
185A ILE* 4.0 2.2 - - - -
186A THR* 3.7 5.2 - - - -
187A SER* 3.5 15.0 - - - +
402A NA 3.5 2.0 - - - -
407A ATP 3.2 37.7 + - - +
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Residues in contact with GLN 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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119A LYS* 3.3 23.7 - - + +
150A ASN* 1.3 71.5 - - - +
152A PHE* 1.3 63.5 + - - +
154A ALA* 3.0 8.1 + - - +
155A GLU* 2.9 48.6 + - - +
162A ILE* 3.3 35.3 + - + -
185A ILE* 3.7 8.2 - - + +
187A SER 2.9 19.8 + - - +
188A SER* 3.4 11.0 - - - -
189A ASP* 2.6 43.8 + - - +
190A LEU* 4.2 3.9 + - - +
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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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117A GLY* 3.6 22.9 - - - -
118A ASP 3.8 6.1 - - - -
119A LYS* 3.3 31.6 - - + +
123A GLU* 3.9 19.7 - - - -
124A GLY 4.1 20.2 - - - -
125A SER* 4.0 11.9 - - - -
126A MET* 3.8 18.2 - - + -
150A ASN* 3.2 7.5 + - - +
151A GLN* 1.3 79.6 - - - +
153A GLU* 1.3 58.1 + - + +
155A GLU* 3.4 18.0 + - + +
156A LEU* 3.1 61.4 + - + +
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Residues in contact with GLU 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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113A ASP* 4.7 0.2 - - - +
114A PRO* 3.1 19.0 - - + +
115A VAL* 3.0 9.9 - - - +
116A LEU* 2.6 32.4 + - + +
117A GLY 3.3 23.1 + - - +
148A THR 4.5 0.2 - - - +
149A PRO* 3.5 20.3 - - + +
150A ASN* 2.8 36.3 + - - +
152A PHE* 1.3 70.9 - - + +
154A ALA* 1.3 60.4 + - - +
155A GLU 3.1 1.8 - - - -
156A LEU* 4.0 6.1 - - - +
157A LEU* 3.1 35.3 + - - +
402A NA 3.9 0.3 - - - -
407A ATP 2.5 27.2 + - - -
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Residues in contact with ALA 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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149A PRO* 4.0 18.1 - - + +
150A ASN 3.0 10.8 + - - +
151A GLN 3.0 9.5 + - - +
153A GLU* 1.3 77.0 - - - +
155A GLU* 1.3 59.0 + - - +
157A LEU* 3.9 3.0 + - - +
158A SER* 2.9 25.1 + - - -
162A ILE* 4.5 2.9 - - + -
171A VAL* 3.2 20.2 - - + +
175A LEU* 4.4 10.6 - - + +
185A ILE* 4.3 20.4 - - + -
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Residues in contact with GLU 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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119A LYS* 3.5 16.4 + - - -
123A GLU* 4.8 4.9 - - - +
151A GLN* 2.9 39.0 + - - +
152A PHE* 3.6 22.7 - - + +
153A GLU 3.1 0.2 - - - -
154A ALA* 1.3 76.9 - - - +
156A LEU* 1.3 57.0 + - + +
158A SER* 3.6 0.2 + - - -
159A GLY* 2.7 35.9 + - - -
160A ARG 3.6 21.4 + - - +
161A LYS* 3.6 16.6 - - + +
162A ILE* 2.9 33.0 + - + +
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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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116A LEU* 4.1 13.5 - - + -
126A MET* 3.6 34.5 - - + -
133A LEU* 3.8 34.1 - - + +
137A LYS* 4.0 8.5 + - - +
152A PHE* 3.1 57.6 + - + +
153A GLU 3.5 4.2 + - - +
155A GLU* 1.3 78.9 - - + +
157A LEU* 1.3 59.2 + - - +
158A SER 3.4 0.3 + - - -
159A GLY* 4.0 5.1 + - - -
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Residues in contact with LEU 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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114A PRO* 4.1 24.5 - - + -
116A LEU* 4.0 19.5 - - + -
133A LEU* 4.5 2.0 - - + -
136A TYR* 4.0 23.6 - - + -
137A LYS* 3.6 32.4 - - + +
141A VAL* 4.0 24.2 - - + -
147A ILE* 5.3 3.6 - - + -
149A PRO* 4.8 6.1 - - + -
153A GLU 3.1 22.9 + - - +
154A ALA* 4.4 2.2 - - - +
155A GLU 3.3 0.2 - - - -
156A LEU* 1.3 76.7 - - - +
158A SER* 1.3 57.0 + - - +
175A LEU* 3.7 23.8 - - + -
178A MET* 4.0 15.2 - - + +
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Residues in contact with SER 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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137A LYS* 6.0 0.2 - - - -
154A ALA 2.9 21.1 + - - -
155A GLU 3.4 1.4 + - - -
157A LEU* 1.3 80.9 - - - +
159A GLY* 1.3 58.7 + - - +
160A ARG* 3.1 20.4 + - - +
171A VAL* 3.2 21.3 - - - +
174A MET* 3.6 38.9 - - - +
175A LEU* 4.6 6.3 - - - -
178A MET* 5.5 1.1 - - - -
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Residues in contact with GLY 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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155A GLU 2.7 18.8 + - - -
156A LEU* 4.0 5.3 + - - -
157A LEU 3.8 0.8 - - - -
158A SER* 1.3 72.4 - - - +
160A ARG* 1.3 68.3 + - - +
161A LYS 3.9 1.6 + - - -
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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