Contacts of the helix formed by residues 151 - 166 (chain Q) in PDB entry 1NVU
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 GLY 151 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142Q ILE* 3.9 3.1 - - - +
143Q GLU 3.9 13.5 - - - -
144Q THR* 3.4 12.8 - - - +
149Q ARG 3.3 1.4 + - - -
150Q GLN* 1.3 75.6 - - - +
152Q VAL* 1.3 62.8 + - - +
153Q GLU 3.5 1.8 - - - -
154Q ASP* 3.3 16.1 + - - +
155Q ALA* 2.9 19.8 + - - +
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Residues in contact with VAL 152 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Q LEU* 3.8 40.6 - - + +
22Q GLN* 4.2 6.1 - - + -
23Q LEU* 4.2 24.0 - - + +
144Q THR* 4.4 4.0 - - - -
145Q SER 3.4 25.6 - - - +
146Q ALA* 4.2 4.5 - - - -
149Q ARG* 3.2 25.1 + - + +
150Q GLN 2.9 7.2 + - - +
151Q GLY* 1.3 78.5 - - - +
153Q GLU* 1.3 65.3 + - + +
155Q ALA* 3.2 8.3 + - - +
156Q PHE* 3.3 21.4 + - + -
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Residues in contact with GLU 153 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Q LEU* 4.2 13.5 - - + -
149Q ARG* 2.9 27.8 + - - +
151Q GLY 3.5 0.2 - - - -
152Q VAL* 1.3 77.8 - - - +
154Q ASP* 1.3 59.2 + - - +
155Q ALA 3.2 0.2 + - - -
156Q PHE 3.3 0.7 + - - -
157Q TYR* 2.8 68.2 + - + +
1007Q PO4 3.6 7.5 + - - +
755S GLN* 3.1 39.0 + - - +
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Residues in contact with ASP 154 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Q ILE* 3.8 21.4 - - + +
151Q GLY* 3.3 17.5 + - - +
152Q VAL 3.2 0.8 - - - -
153Q GLU* 1.3 79.9 - - - +
155Q ALA* 1.3 55.8 + - - +
158Q THR* 2.5 51.6 + - - -
1007Q PO4 2.9 34.7 + - - +
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Residues in contact with ALA 155 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q LEU* 6.3 1.6 - - + -
79Q LEU* 3.7 18.7 - - + +
112Q VAL* 4.0 3.6 - - - +
114Q VAL* 4.2 20.9 - - + -
142Q ILE* 3.8 14.8 - - + +
144Q THR* 4.1 16.2 - - + -
151Q GLY 2.9 17.2 + - - +
152Q VAL 3.6 5.2 - - - +
153Q GLU 3.2 0.2 - - - -
154Q ASP* 1.3 77.2 - - - +
156Q PHE* 1.3 64.1 + - + +
158Q THR* 3.8 2.4 - - - -
159Q LEU 3.2 15.8 + - - -
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Residues in contact with PHE 156 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Q LEU* 3.9 22.8 - - + +
8Q VAL* 4.1 5.2 - - + -
19Q LEU* 3.9 27.8 - - + -
20Q THR* 3.9 25.8 - - - -
23Q LEU* 3.5 31.2 - - + -
53Q LEU* 5.2 0.7 - - + -
55Q ILE* 3.8 26.2 - - + -
79Q LEU* 3.7 28.5 - - + -
152Q VAL* 3.3 23.4 + - + +
153Q GLU 3.3 5.4 + - - +
155Q ALA* 1.3 81.3 - - + +
157Q TYR* 1.3 67.1 - - + +
159Q LEU* 3.2 7.5 + - - +
160Q VAL* 3.0 28.4 + - - +
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Residues in contact with TYR 157 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q LEU* 3.9 14.6 - - + +
42Q LYS* 3.4 24.8 - - - -
44Q VAL* 3.4 21.3 - - + +
45Q VAL 5.7 0.7 - - - -
46Q ILE* 3.5 30.9 - - + +
53Q LEU* 4.1 17.7 - - + -
153Q GLU* 2.8 49.1 + - + +
156Q PHE* 1.3 74.2 - - + +
158Q THR* 1.3 64.7 + - - +
160Q VAL* 3.3 6.2 + - - +
161Q ARG* 3.0 41.4 + - - +
1007Q PO4 3.3 25.4 - - - +
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Residues in contact with THR 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Q VAL* 4.2 3.1 - - + -
140Q PRO* 3.9 29.8 - - + -
142Q ILE* 3.5 10.4 - - + +
154Q ASP* 2.5 41.1 + - - -
155Q ALA 3.8 3.6 - - - -
157Q TYR* 1.3 75.9 - - - +
159Q LEU* 1.3 63.9 + - - +
161Q ARG* 3.1 19.4 + - + +
162Q GLU* 3.0 30.8 + - + +
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Residues in contact with LEU 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q LEU* 4.1 28.0 - - + -
77Q GLY* 3.9 14.8 - - - +
78Q PHE 3.7 21.3 - - - +
79Q LEU* 3.5 23.1 - - + +
110Q PRO* 3.7 7.9 - - + +
111Q MET* 3.7 31.9 - - - +
112Q VAL* 3.7 12.1 - - + +
155Q ALA 3.2 10.4 + - - +
156Q PHE 3.2 9.5 + - - +
158Q THR* 1.3 81.2 - - - +
160Q VAL* 1.3 62.6 + - - +
162Q GLU* 3.1 7.8 + - - +
163Q ILE* 3.0 27.2 + - + +
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Residues in contact with VAL 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 3.8 29.8 - - + -
6Q LEU* 4.2 11.9 - - + -
46Q ILE* 3.8 24.2 - - + -
51Q CYS* 4.3 3.1 - - - -
53Q LEU* 3.8 32.1 - - + -
156Q PHE 3.0 18.7 + - - +
157Q TYR 3.5 7.9 - - - +
159Q LEU* 1.3 75.3 - - - +
161Q ARG* 1.3 64.0 + - - +
163Q ILE* 3.2 11.3 + - - +
164Q ARG* 2.9 29.7 + - - +
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Residues in contact with ARG 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q ILE* 4.0 16.1 - - + +
47Q ASP* 2.8 41.7 + - - +
157Q TYR* 3.0 32.5 + - - +
158Q THR* 3.1 17.8 + - + +
160Q VAL* 1.3 75.2 - - - +
162Q GLU* 1.3 62.4 + - + +
164Q ARG* 3.4 11.9 + - - +
165Q GLN* 3.0 39.0 + - - +
1007Q PO4 2.8 44.4 + - - -
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Residues in contact with GLU 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q PRO* 4.1 14.4 - - + +
111Q MET* 2.6 39.6 + - - +
112Q VAL* 3.9 3.1 - - - +
138Q GLY 5.5 0.7 - - - +
139Q ILE* 4.9 1.9 - - - +
140Q PRO* 3.1 29.8 - - - +
158Q THR* 3.0 20.8 + - + +
159Q LEU* 3.1 6.0 + - - +
161Q ARG* 1.3 75.8 - - + +
163Q ILE* 1.3 65.4 + - - +
165Q GLN* 3.4 5.9 + - - +
166Q HIS* 3.0 25.1 + - - +
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Residues in contact with ILE 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q TYR* 3.6 26.2 - - + -
6Q LEU* 3.3 33.9 - - + -
76Q GLU* 3.9 37.9 - - + +
77Q GLY* 3.7 19.7 - - - +
110Q PRO* 3.9 14.4 - - + -
159Q LEU* 3.0 14.8 + - + +
160Q VAL* 3.6 5.6 - - - +
162Q GLU* 1.3 76.1 - - - +
164Q ARG* 1.3 63.3 + - - +
166Q HIS* 3.4 16.6 + - - +
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Residues in contact with ARG 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Q THR* 5.7 1.2 - - - -
4Q TYR* 2.9 30.7 + - - +
46Q ILE* 3.3 26.0 + - - +
47Q ASP* 3.9 20.3 + - - +
49Q GLU* 3.7 29.3 + - - +
51Q CYS* 2.8 35.7 - - - -
160Q VAL* 2.9 21.0 + - - +
161Q ARG* 3.6 10.1 - - - +
162Q GLU 3.2 0.2 - - - -
163Q ILE* 1.3 79.8 - - - +
165Q GLN* 1.3 63.8 + - + +
166Q HIS* 3.6 4.0 + - - +
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Residues in contact with GLN 165 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161Q ARG* 3.0 26.4 + - - +
162Q GLU* 3.8 5.1 - - - +
164Q ARG* 1.3 81.3 - - + +
166Q HIS* 1.3 63.0 + - - +
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Residues in contact with HIS 166 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106Q SER* 5.3 2.0 + - - -
108Q ASP* 3.0 47.8 + - + -
109Q VAL* 5.5 0.4 - - - -
110Q PRO* 3.7 24.3 - - + +
162Q GLU 3.0 17.1 + - - +
163Q ILE* 3.5 14.0 - - + +
164Q ARG 3.3 4.4 - - - +
165Q GLN* 1.3 84.2 - - - +
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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