Contacts of the helix formed by residues 201 - 209 (chain A) in PDB entry 1V9P
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 ARG 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ASP* 3.2 18.1 + - - +
121A GLY* 2.6 46.7 + - - +
122A LEU* 2.7 40.3 - - + +
123A SER* 4.2 13.7 + - - +
139A ARG* 5.7 5.5 - - - +
174A GLU* 3.9 9.1 + - - -
199A ASN* 2.6 17.1 + - - +
200A PRO* 1.3 70.6 - - - +
202A ASN* 1.3 74.0 + - - +
204A ALA 2.9 6.9 + - - -
205A ALA* 2.9 1.3 + - - +
700A AMP 3.8 36.7 + - - -
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 6.2 0.6 - - - +
197A PHE* 4.2 18.7 - - + -
198A LYS* 5.3 3.8 + - - +
199A ASN* 3.0 29.3 + - - +
201A ARG* 1.3 85.3 - - - +
203A ALA* 1.3 56.0 + - - +
205A ALA* 2.6 36.9 + - - +
206A GLY* 3.0 6.1 + - - -
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A MET* 3.9 13.4 - - - +
182A PHE* 3.6 21.3 - - + -
185A LEU* 4.3 0.7 - - + -
197A PHE* 3.2 36.6 - - + -
199A ASN 3.1 16.0 + - - +
200A PRO* 4.3 2.5 - - + -
202A ASN* 1.3 77.4 - - - +
204A ALA* 1.3 57.2 + - - +
206A GLY 4.3 0.9 - - - -
207A SER* 2.7 28.8 + - - -
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Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY* 5.2 0.2 - - - -
122A LEU* 3.5 13.0 - - + -
175A VAL* 3.9 16.6 - - + +
176A TYR* 4.0 12.8 - - - -
177A MET* 4.0 5.2 - - - +
200A PRO 3.1 20.5 + - - +
201A ARG 2.9 6.1 + - - +
203A ALA* 1.3 76.1 - - - +
205A ALA* 1.3 69.2 + - - +
207A SER* 3.6 2.9 + - - -
208A LEU* 3.3 22.1 + - - +
221A LEU* 4.1 13.6 - - + +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.3 30.2 - - + +
201A ARG 2.9 7.0 + - - +
202A ASN* 2.6 16.7 + - - +
204A ALA* 1.3 76.1 - - - +
206A GLY* 1.3 58.8 + - - +
208A LEU* 3.1 9.5 + - - +
209A ARG* 2.9 45.3 + - - +
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Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A PHE* 4.7 12.3 - - - -
202A ASN 3.0 7.8 + - - -
203A ALA 4.7 0.4 - - - -
205A ALA* 1.3 73.9 - - - +
207A SER* 1.3 53.0 + - - +
208A LEU 2.6 16.8 + - - -
209A ARG* 2.6 20.1 + - - -
210A GLN* 3.2 24.1 + - - +
219A ARG* 4.9 0.9 - - - -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A MET* 3.3 6.1 - - - +
185A LEU* 3.6 1.7 - - - +
197A PHE* 5.1 0.4 - - - -
203A ALA 2.7 24.8 + - - -
204A ALA 3.9 0.9 - - - -
205A ALA 3.4 0.6 - - - -
206A GLY* 1.3 71.5 - - - +
208A LEU* 1.3 50.8 + - - +
210A GLN* 3.9 4.8 - - - +
216A THR* 2.6 39.6 + - - +
219A ARG* 3.3 52.7 + - - +
221A LEU* 3.8 16.6 - - - -
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 5.0 0.2 - - - -
122A LEU* 5.7 6.1 - - + -
124A VAL* 4.5 8.5 - - + -
138A THR* 4.4 14.1 - - + -
148A VAL* 3.1 28.0 - - + +
151A ASN* 2.4 60.6 + - + +
152A LEU* 3.5 30.7 - - + -
155A ILE* 5.3 1.3 - - + -
175A VAL* 4.4 16.6 - - + -
204A ALA 3.3 14.5 + - - +
205A ALA* 3.1 6.9 + - - +
206A GLY 2.6 4.9 + - - -
207A SER* 1.3 74.7 - - - +
209A ARG* 1.3 53.5 + - - +
210A GLN 3.2 0.9 - - - -
216A THR* 3.9 0.7 - - + -
221A LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.9 32.9 - - + -
122A LEU* 4.9 8.3 - - - +
138A THR* 5.1 17.8 + - - +
146A GLU* 3.9 26.6 + - + +
148A VAL* 5.1 1.3 - - - -
205A ALA* 2.9 32.2 + - - +
206A GLY* 2.6 17.7 + - - +
208A LEU* 1.3 69.2 - - - +
210A GLN* 1.3 64.3 + - - +
211A LYS 4.3 0.2 + - - -
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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