Contacts of the helix formed by residues 152 - 164 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C SER* 3.1 35.9 - - - +
24C VAL* 5.0 2.0 - - + +
26C ARG* 4.0 16.2 - - + +
27C THR* 3.9 24.2 - - - +
150C PRO 3.5 5.3 - - - +
151C ASN* 1.3 91.8 - - - +
153C MET* 1.3 59.5 + - - +
155C PHE* 3.2 7.3 + - + +
156C VAL* 3.1 29.2 + - + +
233C PHE* 4.7 11.4 - - + -
234C ASN 5.8 2.9 - - - +
217D ASN 6.0 0.7 - - - +
218D PRO* 6.6 0.2 - - + -
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Residues in contact with MET 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 5.9 0.2 - - - -
151C ASN* 3.5 14.5 + - - +
152C PRO* 1.3 80.3 - - - +
154C ASN* 1.3 68.6 + - - +
156C VAL* 5.1 2.2 - - - -
157C GLY* 3.0 29.1 + - - +
179C PHE* 3.9 20.9 - - + -
227C ASN* 4.0 1.1 - - - +
231C GLN* 3.1 48.7 - - - +
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ILE* 3.7 22.4 - - + +
151C ASN* 2.9 21.3 + - + +
153C MET* 1.3 87.6 - - - +
155C PHE* 1.3 60.6 + - - +
157C GLY 4.2 0.2 - - - -
158C THR* 3.0 25.6 + - - -
179C PHE* 3.5 33.5 - - + +
180C PHE* 3.7 17.3 - - + -
226C ASN* 3.7 1.9 - - - +
227C ASN* 2.9 41.4 + - - +
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Residues in contact with PHE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 6.0 0.7 - - + -
11C TYR* 4.5 7.6 - + - -
23C SER* 6.0 0.7 - - - +
24C VAL* 3.7 35.0 - - + -
35C LEU* 5.6 3.8 - - + -
42C MET* 6.4 1.3 - - + -
71C VAL* 3.7 40.8 - - + -
107C ILE* 3.8 24.9 - - + -
109C ILE* 4.0 22.4 - - + -
145C ILE* 4.0 13.0 - - + +
150C PRO* 5.5 1.3 - - + -
151C ASN 3.6 4.9 + - - +
152C PRO* 3.2 7.3 + - + +
154C ASN* 1.3 79.0 - - - +
156C VAL* 1.3 76.6 + - + +
158C THR* 3.0 6.1 + - - -
159C VAL* 3.0 38.5 + - + +
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.8 4.0 - - + +
27C THR* 3.5 37.5 - - + +
30C PRO* 4.1 21.8 - - + -
35C LEU* 4.4 19.7 - - + -
152C PRO* 3.1 15.1 + - + +
153C MET* 4.7 1.8 - - - +
155C PHE* 1.3 89.3 - - + +
157C GLY* 1.3 57.4 + - - +
159C VAL* 3.8 5.7 - - - +
160C VAL* 3.0 40.7 + - + +
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Residues in contact with GLY 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 3.0 21.8 + - - +
156C VAL* 1.3 77.0 - - - +
158C THR* 1.3 58.5 + - - +
160C VAL* 4.4 5.0 - - - +
161C HIS* 3.2 25.9 + - - +
165C LYS* 5.1 1.6 + - - -
178C MET* 5.2 1.9 - - - +
179C PHE* 4.0 15.2 - - - -
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Residues in contact with THR 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE* 4.0 16.6 - - + -
143C ILE* 4.0 22.9 - - + -
145C ILE* 3.7 21.4 - - + +
154C ASN 3.0 22.2 + - - -
155C PHE 3.0 5.1 + - - -
157C GLY* 1.3 77.6 - - - +
159C VAL* 1.3 65.2 + - - +
161C HIS* 3.5 5.3 + - - +
162C LEU* 2.9 27.6 + - + +
168C PRO* 4.7 8.5 - - + +
176C PRO* 3.7 8.7 - - - +
178C MET* 5.3 1.1 - - - -
179C PHE* 3.3 13.3 - - - -
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Residues in contact with VAL 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 5.6 7.0 - - + -
35C LEU* 5.1 7.2 - - + -
39C VAL* 5.4 0.2 - - + -
40C ILE* 4.0 19.3 - - + -
69C VAL* 5.5 4.3 - - + -
71C VAL* 5.2 4.3 - - + -
107C ILE* 3.7 24.0 - - + -
155C PHE* 3.0 33.3 + - + +
156C VAL* 3.4 9.6 + - - +
158C THR* 1.3 76.0 - - - +
160C VAL* 1.3 72.5 + - + +
162C LEU* 3.1 7.2 + - + +
163C LEU* 3.0 42.8 + - + +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 5.4 6.7 - - + -
35C LEU* 5.1 2.9 - - + -
39C VAL* 4.5 19.3 - - + -
156C VAL* 3.0 30.9 + - + +
157C GLY* 4.4 4.9 - - - +
159C VAL* 1.3 84.5 - - + +
161C HIS* 1.3 54.7 + - - +
163C LEU* 3.3 7.3 + - - -
164C THR* 2.7 49.2 + - + +
165C LYS* 5.9 2.9 - - - +
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Residues in contact with HIS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C GLY 3.2 21.5 + - - +
158C THR* 3.5 7.9 - - - +
160C VAL* 1.3 76.7 - - - +
162C LEU* 1.3 61.8 + - - +
164C THR* 3.6 4.5 - - - -
165C LYS* 2.7 80.9 + - + +
166C GLY 2.8 33.9 + - - -
167C MET 3.9 3.1 - - - -
168C PRO* 3.5 36.5 - - + +
178C MET* 4.6 15.4 - - + +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C VAL* 4.6 11.0 - - + -
105C ALA* 4.1 21.1 - - + -
107C ILE* 3.7 29.6 - - + -
143C ILE* 3.9 26.7 - - + -
158C THR 3.1 13.0 - - - +
159C VAL* 3.2 6.5 - - + +
161C HIS* 1.3 82.7 + - - +
163C LEU* 1.3 64.2 + - + +
166C GLY* 3.3 30.2 + - - +
167C MET* 4.1 16.8 - - - +
168C PRO* 4.1 2.0 - - + -
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO* 3.6 39.5 - - + -
9C VAL* 6.4 1.3 - - + -
39C VAL* 4.1 15.0 - - + +
40C ILE* 3.9 19.5 - - + -
69C VAL* 4.8 17.3 - - + -
159C VAL* 3.0 26.9 + - + +
160C VAL* 3.7 6.3 - - - +
162C LEU* 1.3 82.8 - - + +
164C THR* 1.3 66.3 + - + +
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Residues in contact with THR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 2.7 39.0 + - + +
161C HIS 3.5 0.5 + - - -
162C LEU 4.9 0.2 - - - -
163C LEU* 1.3 86.6 - - + +
165C LYS* 1.3 92.7 + - - +
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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
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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