Contacts of the helix formed by residues 150 - 159 (chain B) in PDB entry 1RFV
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY 2.6 25.8 + - - -
118B ASP* 3.7 10.7 - - - +
149B PRO* 1.3 75.6 - - - +
151B GLN* 1.3 65.9 + - - +
152B PHE* 3.2 6.9 + - - +
153B GLU* 2.6 55.7 + - - +
154B ALA* 2.9 19.9 + - - +
185B ILE* 4.0 3.6 - - - -
186B THR* 3.9 3.6 - - - -
187B SER* 3.8 11.4 - - - +
1401B ADP 3.1 39.9 + - - +
1402B ZN 4.4 1.0 - - - -
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Residues in contact with GLN 151 (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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119B GLN* 3.2 16.8 - - + +
150B ASN* 1.3 70.8 - - - +
152B PHE* 1.3 63.8 + - - +
154B ALA* 3.1 6.4 + - - +
155B GLU* 3.0 50.1 + - - +
162B ILE* 3.6 36.7 + - + -
185B ILE* 3.8 9.1 - - + +
187B SER 3.0 19.5 + - - +
188B SER* 3.3 12.9 - - - -
189B ASN* 2.7 43.0 + - - +
190B LEU* 3.9 6.4 + - + +
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Residues in contact with PHE 152 (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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116B MET 4.4 0.2 - - - -
117B GLY* 3.5 37.2 - - - -
118B ASP* 3.7 9.6 - - - -
119B GLN* 3.3 31.5 - - + +
124B GLY* 3.5 31.0 - - - -
125B ALA 4.0 4.9 - - - -
126B MET* 3.9 22.7 - - + -
150B ASN* 3.2 7.0 + - - +
151B GLN* 1.3 79.1 - - - +
153B GLU* 1.3 61.9 + - + +
155B GLU* 3.3 9.6 + - + +
156B LEU* 3.2 58.2 + - + +
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Residues in contact with GLU 153 (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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113B ASP* 4.2 1.2 - - - +
114B PRO* 3.1 23.8 - - + +
115B VAL* 3.2 8.7 - - - +
116B MET* 3.0 39.4 + - + +
117B GLY 3.2 16.3 + - - +
149B PRO* 3.3 20.0 - - + +
150B ASN* 2.6 43.1 + - - +
152B PHE* 1.3 72.2 - - + +
154B ALA* 1.3 65.5 + - - +
156B LEU* 3.4 3.3 + - - +
157B LEU* 3.1 28.6 + - - +
1402B ZN 4.0 11.7 - - - -
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Residues in contact with ALA 154 (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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149B PRO* 3.9 15.2 - - + +
150B ASN 2.9 13.2 + - - +
151B GLN* 3.5 9.4 - - - +
153B GLU* 1.3 77.2 - - - +
155B GLU* 1.3 60.4 + - - +
157B LEU* 3.6 3.5 + - - +
158B THR* 3.0 31.2 + - - +
162B ILE* 4.6 2.7 - - + -
171B VAL* 3.8 14.2 - - + +
175B LEU* 4.5 7.4 - - + -
185B ILE* 4.1 25.1 - - + -
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Residues in contact with GLU 155 (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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119B GLN* 3.2 26.0 + - - +
151B GLN* 3.0 32.5 + - - +
152B PHE* 3.5 11.6 - - + +
153B GLU 3.2 0.2 - - - -
154B ALA* 1.3 74.7 - - - +
156B LEU* 1.3 55.8 + - + +
158B THR* 3.3 1.0 + - - -
159B GLY* 2.7 33.8 + - - -
160B ARG 3.1 25.7 + - - +
161B LYS* 3.9 24.1 - - + +
162B ILE* 3.0 35.9 + - + +
171B VAL* 5.3 0.9 - - - -
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Residues in contact with LEU 156 (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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116B MET* 4.2 21.8 - - + -
126B MET* 4.0 24.2 - - + -
133B LEU* 3.7 24.6 - - + +
137B ARG* 3.5 22.2 + - - -
152B PHE* 3.2 50.6 + - + +
153B GLU* 3.4 5.6 + - - +
155B GLU* 1.3 80.7 - - + +
157B LEU* 1.3 62.1 + - - +
158B THR 3.3 0.3 + - - -
159B GLY* 3.4 7.5 + - - -
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Residues in contact with LEU 157 (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 PRO* 4.2 22.4 - - + -
116B MET* 4.0 11.4 - - + -
133B LEU* 4.3 3.6 - - + -
136B TYR* 3.9 22.2 - - + -
137B ARG* 3.4 36.7 - - + +
141B VAL* 3.8 29.6 - - + -
147B ILE* 5.0 4.9 - - + -
149B PRO* 4.6 6.1 - - + -
153B GLU 3.1 22.7 + - - +
154B ALA* 3.9 4.5 - - - +
155B GLU 3.3 0.4 - - - -
156B LEU* 1.3 76.2 - - - +
158B THR* 1.3 59.7 + - - +
175B LEU* 4.1 23.6 - - + -
178B MET* 3.7 10.8 - - + +
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Residues in contact with THR 158 (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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137B ARG* 5.9 0.7 - - - -
154B ALA 3.0 15.5 + - - +
155B GLU* 3.3 1.8 + - - -
156B LEU 3.2 0.2 - - - -
157B LEU* 1.3 77.7 - - - +
159B GLY* 1.3 62.8 + - - +
160B ARG* 3.0 14.2 + - - +
171B VAL* 3.5 23.1 - - + +
174B MET* 3.8 36.8 - - + +
175B LEU* 3.6 35.7 - - + -
178B MET* 4.4 5.8 - - - -
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Residues in contact with GLY 159 (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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137B ARG* 5.4 6.0 - - - +
155B GLU 2.7 14.3 + - - -
156B LEU* 3.4 9.7 + - - -
157B LEU 3.5 0.2 - - - -
158B THR* 1.3 73.6 - - - +
160B ARG* 1.3 58.2 + - - +
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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