Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 2FRV
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 PRO 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER* 3.1 37.0 - - - +
24A VAL* 5.0 1.8 - - - +
26A ARG* 4.0 15.5 - - + +
27A THR* 3.9 25.4 - - - +
150A PRO 3.5 5.3 - - - +
151A ASN* 1.3 91.0 - - - +
153A MET* 1.3 60.4 + - - +
155A PHE* 3.2 7.3 + - + +
156A VAL* 3.1 29.4 + - + +
233A PHE* 4.7 11.4 - - + -
234A ASN 5.8 2.9 - - - +
217B ASN 6.0 1.1 - - - +
218B PRO* 6.6 0.2 - - + -
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Residues in contact with MET 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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27A THR* 5.9 0.4 - - - -
151A ASN* 3.5 14.9 + - - +
152A PRO* 1.3 79.1 - - - +
154A ASN* 1.3 67.0 + - - +
156A VAL* 5.1 2.2 - - - -
157A GLY* 3.0 29.7 + - - +
179A PHE* 3.9 20.1 - - + -
227A ASN* 4.0 1.3 - - - +
231A GLN* 3.1 49.4 - - + +
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Residues in contact with ASN 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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145A ILE* 3.7 22.4 - - + +
151A ASN* 2.9 21.1 + - + +
153A MET* 1.3 87.6 - - - +
155A PHE* 1.3 60.6 + - - +
157A GLY 4.2 0.2 - - - -
158A THR* 3.0 26.2 + - - -
179A PHE* 3.5 32.0 - - + +
180A PHE* 3.7 16.5 - - + -
226A ASN* 3.7 2.3 - - - +
227A ASN* 2.9 42.1 + - - +
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Residues in contact with PHE 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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9A VAL* 6.0 0.4 - - + -
11A TYR* 4.5 8.3 - + - -
23A SER* 6.0 0.7 - - - +
24A VAL* 3.7 35.4 - - + -
35A LEU* 5.6 4.3 - - + -
42A MET* 6.4 1.6 - - + -
71A VAL* 3.7 41.7 - - + -
107A ILE* 3.8 23.8 - - + -
109A ILE* 4.0 22.9 - - + -
145A ILE* 4.1 13.7 - - + -
150A PRO* 5.5 1.6 - - + -
151A ASN 3.6 4.8 + - - +
152A PRO* 3.2 7.8 + - + +
154A ASN* 1.3 79.2 - - - +
156A VAL* 1.3 76.1 + - + +
158A THR* 3.0 5.5 + - - -
159A VAL* 3.0 37.6 + - + +
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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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24A VAL* 4.8 3.6 - - + -
27A THR* 3.5 37.0 - - + +
30A PRO* 4.1 22.2 - - + -
35A LEU* 4.4 20.0 - - + -
152A PRO* 3.1 15.1 + - + +
153A MET* 4.7 2.0 - - - +
155A PHE* 1.3 90.2 - - + +
157A GLY* 1.3 58.5 + - - +
159A VAL* 3.8 5.4 - - - +
160A VAL* 3.0 40.1 + - + +
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Residues in contact with GLY 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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153A MET* 3.0 21.5 + - - -
156A VAL* 1.3 77.8 - - - +
158A THR* 1.3 58.1 + - - +
160A VAL* 4.2 5.3 - - - +
161A HIS* 3.2 25.7 + - - +
165A LYS* 5.1 1.9 + - - -
178A MET* 5.2 1.4 - - - +
179A PHE* 4.0 16.7 - - - -
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Residues in contact with THR 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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107A ILE* 4.0 16.8 - - + -
143A ILE* 4.0 23.1 - - + -
145A ILE* 3.7 21.2 - - + +
154A ASN 3.0 22.3 + - - -
155A PHE 3.0 4.9 + - - -
157A GLY* 1.3 77.8 - - - +
159A VAL* 1.3 66.2 + - - +
161A HIS* 3.5 5.9 - - - +
162A LEU* 2.9 27.1 + - + +
168A PRO* 4.7 8.3 - - + +
176A PRO* 3.7 8.5 - - - +
178A MET* 5.3 1.1 - - - -
179A PHE* 3.3 13.7 - - - -
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Residues in contact with VAL 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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9A VAL* 5.6 6.7 - - + -
35A LEU* 5.1 7.0 - - + -
39A VAL* 5.4 0.2 - - + -
40A ILE* 4.0 18.8 - - + -
69A VAL* 5.5 4.3 - - + -
71A VAL* 5.2 4.3 - - + -
107A ILE* 3.7 23.8 - - + -
155A PHE* 3.0 33.1 + - + +
156A VAL* 3.4 9.6 + - - +
158A THR* 1.3 76.1 - - - +
160A VAL* 1.3 72.4 + - + +
162A LEU* 3.1 7.9 + - + +
163A LEU* 3.0 42.8 + - + +
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Residues in contact with VAL 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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30A PRO* 5.4 6.3 - - + -
35A LEU* 5.1 2.9 - - + -
39A VAL* 4.5 18.6 - - + -
156A VAL* 3.0 30.9 + - + +
157A GLY* 4.4 5.4 - - - +
159A VAL* 1.3 84.7 - - + +
161A HIS* 1.3 55.5 + - - +
163A LEU* 3.3 6.9 + - - -
164A THR* 2.7 50.9 + - + +
165A LYS* 5.9 2.2 - - - +
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Residues in contact with HIS 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLY 3.2 21.3 + - - +
158A THR* 3.5 7.9 - - - +
159A VAL 3.1 0.6 - - - -
160A VAL* 1.3 76.5 - - - +
162A LEU* 1.3 60.8 + - - +
164A THR* 3.6 5.2 - - - -
165A LYS* 2.7 81.0 + - + +
166A GLY 2.8 33.7 + - - -
167A MET 3.9 2.9 - - - -
168A PRO* 3.5 36.7 - - + +
178A MET* 4.6 15.2 - - + -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.6 10.3 - - + -
105A ALA* 4.1 20.9 - - + -
107A ILE* 3.7 31.4 - - + -
143A ILE* 3.9 27.4 - - + -
158A THR* 3.1 11.4 - - + +
159A VAL* 3.2 6.5 - - + +
161A HIS* 1.3 83.8 - - - +
163A LEU* 1.3 63.4 + - + +
166A GLY* 3.3 29.2 + - - +
167A MET* 4.1 16.6 - - + +
168A PRO* 4.1 2.5 - - + -
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Residues in contact with LEU 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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7A PRO* 3.6 39.7 - - + -
9A VAL* 6.4 1.3 - - + -
39A VAL* 4.1 14.6 - - + +
40A ILE* 3.9 19.3 - - + -
69A VAL* 4.8 17.0 - - + -
159A VAL* 3.0 27.3 + - + +
160A VAL* 3.7 6.5 - - - +
162A LEU* 1.3 81.1 - - + +
164A THR* 1.3 65.0 + - + +
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Residues in contact with THR 164 (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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160A VAL* 2.7 38.6 + - + +
161A HIS 3.5 0.7 + - - -
163A LEU* 1.3 87.9 - - + +
165A LYS* 1.3 92.6 + - - +
166A GLY 3.8 0.2 - - - -
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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