Contacts of the helix formed by residues 164 - 171 (chain M) in PDB entry 1VQN
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 THR 164 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4320 G 4.5 0.4 - - - -
99M ARG* 5.7 0.7 - - - -
102M GLU* 2.7 39.0 + - - +
114M VAL* 3.9 19.5 + - + +
115M LEU 5.1 1.9 + - - -
116M ASN* 5.1 6.1 - - - +
158M ARG* 4.4 12.7 + - - +
159M VAL* 4.0 15.1 - - - +
162M GLY 3.2 1.6 - - - -
163M LEU* 1.3 82.8 - - - +
165M GLY* 1.3 58.0 + - - +
166M ALA 3.0 16.6 - - - +
167M GLY* 3.3 8.5 - - - +
168M ARG* 2.7 36.1 + - - +
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Residues in contact with GLY 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4320 G 3.0 29.6 + - - -
115M LEU 5.3 1.6 + - - -
116M ASN* 4.6 6.7 + - - -
164M THR* 1.3 78.9 - - - +
166M ALA* 1.3 54.9 + - - -
168M ARG* 3.4 6.4 + - - +
169M ARG* 3.0 46.6 + - - +
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Residues in contact with ALA 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96M ASP* 4.3 6.6 - - - +
98M GLN* 3.6 40.4 - - + +
99M ARG* 3.9 6.8 - - - +
102M GLU* 4.0 5.8 - - - +
116M ASN* 5.1 0.4 + - - -
164M THR* 3.0 12.0 - - + +
165M GLY* 1.3 73.6 - - - +
167M GLY* 1.3 65.9 + - - +
169M ARG* 3.6 19.3 - - - +
170M ASN* 3.1 27.4 + - - +
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Residues in contact with GLY 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M ARG* 3.4 24.9 + - - +
162M GLY* 3.4 17.3 - - - -
164M THR* 3.0 15.5 + - - +
166M ALA* 1.3 81.5 - - - +
168M ARG* 1.3 61.6 + - - +
170M ASN* 3.7 2.3 - - - +
171M ARG* 3.1 27.8 + - - +
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Residues in contact with ARG 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1890 A 2.8 40.3 + - - +
1900 G 4.4 14.7 + - - -
4320 G 4.4 5.0 + - - -
4330 C 3.0 37.4 + - - -
4340 U 5.2 5.3 + - - -
155M GLN* 5.9 1.8 - - - +
162M GLY 3.4 8.5 + - - +
163M LEU* 2.9 35.9 + - - +
164M THR 2.7 19.9 + - - +
165M GLY* 3.9 5.8 - - - +
167M GLY* 1.3 69.9 - - - +
169M ARG* 1.3 68.2 + - + +
171M ARG* 3.2 10.0 + - - +
172M GLY 3.6 0.2 + - - -
173M LEU* 3.2 39.1 + - + +
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Residues in contact with ARG 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4000 C 3.9 10.3 + - - +
4300 A 4.8 22.0 + - - -
4310 G 4.3 17.1 + - - -
52M GLN* 5.1 0.4 - - - +
96M ASP* 5.6 0.4 + - - -
98M GLN* 3.4 28.1 + - - +
116M ASN* 4.5 8.1 + - - -
117M SER 4.9 2.4 + - - -
165M GLY* 3.0 22.9 + - - +
166M ALA* 3.6 31.7 - - - +
168M ARG* 1.3 74.3 - - + +
170M ASN* 1.3 54.8 + - - +
172M GLY* 2.6 30.3 + - - -
173M LEU 3.9 0.4 + - - +
174M SER* 4.3 21.9 + - - +
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Residues in contact with ASN 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570 G 3.5 5.4 + - - -
4000 C 2.9 43.9 + - - +
4010 C 3.0 13.8 + - - +
94M ARG 3.1 26.5 + - - +
95M LYS* 3.5 6.9 - - - +
96M ASP* 3.3 17.0 - - - +
99M ARG* 2.8 34.9 - - - +
166M ALA 3.1 16.6 + - - +
167M GLY 3.7 0.4 - - - +
169M ARG* 1.3 78.5 - - - +
171M ARG* 1.3 58.0 + - - +
172M GLY 3.2 1.1 - - - -
187M LEU* 5.4 0.3 - - - +
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Residues in contact with ARG 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550 C 3.1 13.5 + - - -
1560 C 2.6 61.1 + - - +
1570 G 3.9 14.4 - - - +
1880 C 3.3 16.0 + - - -
1890 A 2.6 30.7 + - - -
3990 C 4.9 1.3 - - - -
4000 C 4.8 0.9 - - - -
99M ARG* 4.1 1.8 - - - +
161M ARG 4.4 0.9 - - - -
162M GLY* 3.5 24.8 + - - -
163M LEU* 4.3 2.4 - - - +
167M GLY 3.1 15.5 + - - +
168M ARG* 3.6 7.0 - - - +
169M ARG 2.8 1.4 + - - -
170M ASN* 1.3 76.4 - - - +
172M GLY* 1.3 64.0 + - - +
173M LEU* 3.4 24.0 - - + +
183M THR* 3.4 17.8 - - - +
186M SER* 4.5 3.2 - - - +
187M LEU* 3.7 22.2 - - + +
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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