Contacts of the helix formed by residues 152 - 164 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217L ASN 6.0 0.7 - - - +
218L PRO* 6.3 0.2 - - + -
23S SER* 3.1 36.6 - - - +
24S VAL* 5.1 2.7 - - + -
26S ARG* 4.0 15.5 - - + +
27S THR* 3.9 24.7 - - - +
150S PRO 3.5 5.3 - - - +
151S ASN* 1.3 91.3 - - - +
153S MET* 1.3 59.7 + - - +
155S PHE* 3.2 6.4 + - + +
156S VAL* 3.1 29.8 + - + +
233S PHE* 4.7 11.4 - - + -
234S ASN 5.8 3.8 - - - +
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Residues in contact with MET 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S THR* 5.9 0.7 - - - -
151S ASN* 3.5 14.3 + - - +
152S PRO* 1.3 79.9 - - - +
154S ASN* 1.3 67.1 + - - +
156S VAL* 5.1 2.2 - - - -
157S GLY* 3.0 29.1 + - - +
179S PHE* 3.9 20.7 - - + -
227S ASN* 4.0 1.6 - - - +
231S GLN* 3.1 49.1 - - - +
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Residues in contact with ASN 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145S ILE* 3.7 22.4 - - + +
151S ASN* 2.9 21.6 + - + +
153S MET* 1.3 85.9 - - - +
155S PHE* 1.3 59.9 + - - +
157S GLY 4.2 0.2 - - - -
158S THR* 3.0 26.0 + - - -
179S PHE* 3.5 33.5 - - + +
180S PHE* 3.7 16.7 - - + -
226S ASN* 3.7 1.7 - - - +
227S ASN* 2.9 43.3 + - - +
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Residues in contact with PHE 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S VAL* 6.0 0.7 - - + -
11S TYR* 4.5 7.9 - + - -
23S SER* 6.0 0.9 - - - +
24S VAL* 3.7 35.7 - - + -
35S LEU* 5.6 3.4 - - + -
42S MET* 6.4 1.6 - - + -
71S VAL* 3.7 40.2 - - + -
107S ILE* 3.8 24.0 - - + -
109S ILE* 4.0 23.1 - - + -
145S ILE* 4.0 14.1 - - + +
150S PRO* 5.5 2.0 - - + -
151S ASN 3.6 4.1 + - - +
152S PRO* 3.2 8.0 + - + +
154S ASN* 1.3 78.9 - - - +
156S VAL* 1.3 76.5 + - + +
158S THR* 3.0 6.2 + - - -
159S VAL* 3.0 37.5 + - + +
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Residues in contact with VAL 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S VAL* 4.8 4.0 - - + -
27S THR* 3.5 37.2 - - + +
30S PRO* 4.1 22.0 - - + -
35S LEU* 4.4 19.7 - - + -
152S PRO* 3.1 15.7 + - + +
153S MET* 4.7 1.8 - - - +
155S PHE* 1.3 90.4 - - + +
157S GLY* 1.3 56.2 + - - +
159S VAL* 3.4 5.9 + - - +
160S VAL* 3.0 41.5 + - + +
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Residues in contact with GLY 157 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153S MET* 3.0 21.9 + - - -
156S VAL* 1.3 75.8 - - - +
158S THR* 1.3 59.5 + - - +
160S VAL* 4.4 5.2 - - - +
161S HIS* 3.2 25.4 + - - +
165S LYS* 5.1 1.9 + - - -
178S MET* 5.2 1.7 - - - +
179S PHE* 4.0 16.6 - - - -
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Residues in contact with THR 158 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S ILE* 4.0 16.4 - - + -
143S ILE* 4.0 22.4 - - + -
145S ILE* 3.7 22.4 - - + +
154S ASN 3.0 22.4 + - - -
155S PHE 3.0 5.2 + - - +
157S GLY* 1.3 78.2 - - - +
159S VAL* 1.3 65.8 + - - +
161S HIS* 3.5 5.6 + - - +
162S LEU* 2.9 26.7 + - + +
168S PRO* 4.7 8.6 - - + +
176S PRO* 3.7 8.7 - - - +
178S MET* 5.3 0.8 - - - -
179S PHE* 3.3 13.8 - - - -
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Residues in contact with VAL 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9S VAL* 5.6 6.5 - - + -
35S LEU* 5.1 7.9 - - + -
39S VAL* 5.4 0.2 - - + -
40S ILE* 4.0 18.4 - - + -
69S VAL* 5.5 4.7 - - + -
71S VAL* 5.2 4.0 - - + -
107S ILE* 3.7 23.6 - - + -
155S PHE* 3.0 33.9 + - + +
156S VAL* 3.8 9.6 - - - +
158S THR* 1.3 76.8 - - - +
160S VAL* 1.3 71.6 + - + +
162S LEU* 3.1 7.7 + - + +
163S LEU* 3.0 43.4 + - + +
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Residues in contact with VAL 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S PRO* 5.4 7.2 - - + -
35S LEU* 5.1 2.9 - - + -
39S VAL* 4.5 19.3 - - + -
156S VAL* 3.0 31.6 + - + +
157S GLY* 4.4 5.8 - - - +
159S VAL* 1.3 83.7 - - + +
161S HIS* 1.3 56.2 + - - +
163S LEU* 3.6 6.9 - - - -
164S THR* 2.7 49.8 + - + +
165S LYS* 5.9 2.7 - - - +
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Residues in contact with HIS 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157S GLY 3.2 21.4 + - - +
158S THR* 3.5 8.1 - - - +
159S VAL 3.1 0.6 - - - -
160S VAL* 1.3 76.1 - - - +
162S LEU* 1.3 62.2 + - - +
164S THR* 3.6 4.9 - - - -
165S LYS* 2.7 80.0 + - + +
166S GLY 2.8 33.7 + - - -
167S MET 3.9 3.4 - - - -
168S PRO* 3.5 37.3 - - + +
178S MET* 4.6 17.2 - - + +
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Residues in contact with LEU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69S VAL* 4.6 10.3 - - + -
105S ALA* 4.1 21.3 - - + -
107S ILE* 3.7 31.2 - - + -
143S ILE* 3.9 26.5 - - + -
158S THR* 2.9 12.7 + - + +
159S VAL* 3.2 6.5 - - + +
161S HIS* 1.3 82.8 + - - +
163S LEU* 1.3 64.2 + - + +
166S GLY* 3.3 28.5 + - - +
167S MET* 4.1 16.2 - - + +
168S PRO* 4.1 2.2 - - + -
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Residues in contact with LEU 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7S PRO* 3.6 39.3 - - + -
9S VAL* 6.4 1.1 - - + -
39S VAL* 4.1 15.0 - - + +
40S ILE* 3.9 19.3 - - + -
69S VAL* 4.8 17.9 - - + -
159S VAL* 3.0 27.2 + - + +
160S VAL* 3.7 6.3 - - - +
162S LEU* 1.3 82.3 - - + +
164S THR* 1.3 66.1 + - + +
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Residues in contact with THR 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160S VAL* 2.7 38.6 + - + +
161S HIS 3.5 0.5 + - - -
163S LEU* 1.3 87.2 - - + +
165S LYS* 1.3 91.8 + - - +
166S GLY 3.8 0.4 - - - -
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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