Contacts of the helix formed by residues 145 - 158 (chain B) in PDB entry 3OVS
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 GLU 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B ARG 4.0 10.4 - - - +
51B ASN* 4.0 34.3 + - + +
52B THR* 3.9 7.0 - - + +
141B ILE* 2.8 36.4 + - + +
142B LYS* 3.4 5.9 - - - +
143B GLY 2.7 51.3 + - - +
144B LYS* 1.3 68.9 - - - +
146B ASN* 1.3 59.4 + - - +
147B GLU* 3.2 4.3 - - - +
148B VAL* 3.3 24.0 + - - +
149B ARG* 3.6 9.6 - - - +
179B ILE* 5.7 0.4 - - - -
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Residues in contact with ASN 146 (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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11B LEU* 3.9 15.9 - - + +
15B ILE* 3.4 27.2 - - - +
51B ASN 5.4 0.4 + - - -
143B GLY 4.9 1.9 - - - +
144B LYS* 2.9 14.2 - - + +
145B GLU* 1.3 81.3 + - - +
147B GLU* 1.3 57.1 + - - +
148B VAL 3.0 5.6 - - - -
149B ARG* 3.3 34.9 - - - +
150B LEU* 3.0 35.3 + - + +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 5.1 7.7 - - - +
144B LYS* 3.1 44.3 + - + +
146B ASN* 1.3 76.3 - - - +
148B VAL* 1.3 59.4 + - - +
150B LEU* 4.2 12.8 - - - +
151B LEU* 3.6 5.4 + - - +
179B ILE* 3.4 24.6 - - + +
183B GLY 4.7 2.7 - - - +
184B SER* 3.2 21.2 - - - -
185B PHE* 2.7 62.3 + - - +
186B LEU* 3.9 2.9 + - - +
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 4.2 8.1 - - + -
141B ILE* 3.8 28.0 - - + -
145B GLU 3.3 13.4 + - - +
146B ASN 3.0 0.4 - - - -
147B GLU* 1.3 76.0 - - - +
149B ARG* 1.3 55.1 + - - +
150B LEU 3.1 1.6 - - - -
151B LEU* 2.8 7.8 + - - +
152B LYS* 2.7 54.8 + - + +
175B CYS* 4.3 7.0 - - + -
176B GLU* 3.6 30.7 - - + -
179B ILE* 3.6 22.9 - - + -
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Residues in contact with ARG 149 (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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14B VAL* 3.4 30.6 + - + +
15B ILE* 3.6 19.6 - - - +
16B PRO* 3.2 30.4 - - - +
51B ASN* 3.3 23.1 + - - +
52B THR* 3.9 13.0 - - - +
53B TRP* 2.8 57.9 + - - +
54B LEU* 3.9 4.6 - - + +
145B GLU 3.6 11.7 - - - +
146B ASN* 3.3 28.6 + - - +
148B VAL* 1.3 74.5 - - - +
150B LEU* 1.3 56.2 + - - +
152B LYS* 4.0 9.6 - - - -
153B GLY 3.1 18.7 + - - -
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Residues in contact with LEU 150 (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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7B LEU* 3.8 26.9 - - + +
10B ALA* 3.8 29.6 - - + -
11B LEU* 3.7 29.4 - - + +
14B VAL* 4.5 3.8 - - + -
146B ASN* 3.0 21.9 + - + +
147B GLU* 4.4 18.8 - - - +
149B ARG* 1.3 75.0 - - - +
151B LEU* 1.3 55.8 + - - +
154B PHE* 2.7 37.0 + - - +
185B PHE* 4.2 21.5 - - + -
254B PHE* 3.2 20.0 - - + -
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Residues in contact with LEU 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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147B GLU 3.6 11.4 + - - +
148B VAL 2.8 9.4 + - - +
150B LEU* 1.3 78.4 - - - +
152B LYS* 1.3 62.2 + - - +
154B PHE* 3.2 4.3 - - + +
155B LEU* 3.0 40.2 + - + +
175B CYS* 3.5 45.5 - - + +
178B LEU* 4.4 16.4 - - + -
179B ILE* 3.9 15.9 - - + -
185B PHE* 3.7 25.7 - - + -
188B THR* 4.9 6.5 - - + -
189B VAL* 5.7 0.4 - - + -
238B PHE* 4.3 22.0 - - + -
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Residues in contact with LYS 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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47B SER* 3.2 12.9 + - - -
52B THR* 2.7 34.8 + - - +
53B TRP* 5.2 1.3 - - - -
54B LEU* 4.7 10.5 - - + +
148B VAL* 2.7 40.7 + - + +
149B ARG* 4.0 7.0 - - - +
151B LEU* 1.3 71.7 - - - +
153B GLY* 1.3 52.8 + - - +
155B LEU* 3.1 5.3 + - - +
156B LYS* 2.7 38.3 + - + +
161B TYR* 3.3 39.7 - - + +
172B GLY 4.2 12.3 - - - -
175B CYS* 4.3 5.8 - - - -
176B GLU* 4.2 4.9 + - - -
502B CTP 2.9 27.6 + - - +
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Residues in contact with GLY 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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14B VAL* 4.3 8.3 - - - -
54B LEU* 3.8 17.8 - - - +
149B ARG 3.1 14.3 + - - -
150B LEU 3.6 2.9 - - - -
152B LYS* 1.3 78.7 - - - +
154B PHE* 1.3 62.0 + - - +
156B LYS* 3.9 4.2 - - - +
157B ALA* 3.0 27.5 + - - +
254B PHE* 4.1 10.3 - - - +
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Residues in contact with PHE 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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150B LEU 2.7 17.1 + - - +
151B LEU 3.2 11.2 - - - +
153B GLY* 1.3 74.8 - - - +
155B LEU* 1.3 62.2 + - + +
157B ALA* 3.5 1.4 + - - +
158B ASN* 3.1 36.4 + - - -
160B ILE* 6.4 0.2 - - + -
185B PHE* 3.6 30.7 - + + -
189B VAL* 4.9 0.9 - - + -
238B PHE* 3.9 33.9 - + - -
241B LEU* 4.5 14.6 - - + -
242B CYS* 4.3 11.0 - - - -
245B PHE* 4.2 28.7 - + + -
253B PHE* 3.7 37.0 - + + -
254B PHE* 3.7 14.0 - + - -
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Residues in contact with LEU 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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151B LEU* 3.0 30.8 + - + +
152B LYS 3.7 2.7 - - - +
154B PHE* 1.3 74.8 - - + +
156B LYS* 1.3 62.0 + - - +
158B ASN* 3.4 4.4 + - - -
160B ILE* 3.0 40.0 + - + +
161B TYR* 3.1 18.4 + - + -
170B PHE* 3.5 37.0 - - + -
175B CYS* 3.4 33.7 - - - -
238B PHE* 3.4 35.9 - - + -
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Residues in contact with LYS 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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54B LEU* 3.8 25.2 - - + +
56B GLY 6.1 0.2 - - - -
57B SER* 3.5 22.0 + - - +
152B LYS* 2.7 22.8 + - + +
153B GLY* 4.0 5.2 - - - +
155B LEU* 1.3 71.6 - - - +
157B ALA* 1.3 66.1 + - - +
158B ASN 3.2 0.7 + - - -
159B GLY* 3.3 11.4 + - - -
161B TYR* 3.6 35.8 - - + +
256B PRO* 5.4 2.4 - - - +
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Residues in contact with ALA 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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153B GLY 3.0 18.8 + - - +
154B PHE 3.8 0.2 - - - +
156B LYS* 1.3 76.6 - - - +
158B ASN* 1.3 61.0 + - - +
159B GLY 3.4 1.1 + - - -
253B PHE 3.8 12.6 - - - +
254B PHE 3.5 29.6 - - - +
255B LYS 3.7 12.4 - - - +
256B PRO* 3.8 26.2 - - + +
257B LYS* 4.4 4.0 + - - +
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Residues in contact with ASN 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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154B PHE* 3.1 31.8 + - - +
155B LEU 3.4 4.3 + - - +
156B LYS 3.1 1.2 - - - -
157B ALA* 1.3 80.4 - - - +
159B GLY* 1.3 58.6 + - - +
160B ILE* 3.2 24.6 + - + +
241B LEU* 3.5 38.9 - - + +
253B PHE* 3.7 21.1 + - - +
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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