Contacts of the helix formed by residues 194 - 201 (chain A) in PDB entry 4H1V
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 SER 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A THR* 5.6 3.8 - - - +
184A VAL 4.4 0.3 + - - -
185A THR* 3.4 32.5 - - - -
189A THR* 5.7 1.8 - - - -
190A ASP 3.7 3.5 + - - -
191A MET* 3.4 16.8 + - - -
192A ALA 3.6 0.6 - - - -
193A THR* 1.3 78.6 + - - +
195A GLU* 1.3 63.0 + - - +
196A ALA* 3.3 19.2 + - - +
197A LEU* 3.7 12.3 + - - +
198A LYS* 3.2 23.0 + - - +
201A ARG* 5.5 0.4 + - - +
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Residues in contact with GLU 195 (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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33A THR* 4.5 6.9 - - - +
150A MET* 3.6 17.2 - - + +
151A THR 3.7 23.3 - - - +
152A LYS* 3.8 16.5 + - - +
154A PRO* 3.4 31.9 - - - +
167A ARG* 3.1 25.2 + - - +
193A THR 3.3 5.8 + - - +
194A SER* 1.3 72.0 + - - +
196A ALA* 1.3 59.0 + - - +
198A LYS* 3.3 31.9 + - - +
199A ILE* 3.0 32.2 + - - +
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Residues in contact with ALA 196 (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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31A VAL* 3.8 23.1 - - + +
32A GLY* 4.3 3.4 - - - -
33A THR* 4.8 3.0 - - - +
150A MET* 3.6 14.6 - - + +
183A ALA* 4.4 5.4 - - + -
184A VAL 3.6 23.6 - - - +
194A SER* 3.1 12.2 + - - +
195A GLU* 1.3 79.3 - - - +
197A LEU* 1.3 57.3 + - + +
199A ILE* 3.5 3.5 - - - +
200A SER* 2.7 33.6 + - - -
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Residues in contact with LEU 197 (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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183A ALA* 3.7 23.3 - - + -
185A THR* 4.5 8.1 - - + -
191A MET 3.3 26.9 - - - +
192A ALA* 5.2 0.4 - - - -
194A SER* 3.4 15.8 + - - +
195A GLU 3.4 0.2 - - - -
196A ALA* 1.3 75.9 - - - +
198A LYS* 1.3 61.6 - - - +
200A SER* 3.3 6.1 + - - -
201A ARG* 3.1 49.9 + - - +
210A THR* 5.0 1.8 - - + -
212A ALA* 4.5 10.8 - - + -
235A ILE* 3.7 40.8 - - + -
237A VAL* 4.5 9.6 - - + -
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Residues in contact with LYS 198 (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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154A PRO* 4.4 10.1 - - - +
192A ALA 5.2 1.6 - - - +
193A THR* 3.7 22.9 + - - +
194A SER 3.2 21.0 + - - +
195A GLU* 3.3 29.1 + - - +
197A LEU* 1.3 75.0 - - - +
199A ILE* 1.3 64.3 + - - +
200A SER 3.3 0.3 + - - -
201A ARG* 3.3 35.3 + - - +
202A GLU* 3.4 17.4 + - - +
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Residues in contact with ILE 199 (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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31A VAL* 4.0 18.8 - - + -
150A MET* 3.9 20.9 - - - -
167A ARG* 3.9 42.6 - - + +
170A ILE* 4.1 14.4 - - + -
171A LEU* 4.0 19.7 - - + +
174A ILE* 3.6 11.2 - - + +
195A GLU 3.0 16.3 + - - +
196A ALA 3.5 11.7 - - - +
198A LYS* 1.3 78.2 - - - +
200A SER* 1.3 64.6 + - - +
202A GLU* 3.3 23.0 + - + +
203A VAL 4.2 0.5 + - - -
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Residues in contact with SER 200 (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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31A VAL* 4.6 2.6 - - - +
174A ILE* 4.1 9.2 - - - +
181A ILE* 3.3 32.5 - - - +
183A ALA* 4.3 3.8 - - - +
196A ALA 2.7 21.6 + - - -
197A LEU* 3.5 9.6 - - - -
198A LYS 3.1 0.4 - - - -
199A ILE* 1.3 78.1 - - - +
201A ARG* 1.3 56.1 + - - +
202A GLU 3.0 5.3 + - - -
203A VAL* 3.4 4.5 + - - +
204A ASP* 2.9 32.0 + - - +
210A THR* 4.3 12.8 - - - -
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Residues in contact with ARG 201 (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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192A ALA* 4.7 16.0 + - - +
197A LEU* 3.1 39.5 + - - +
198A LYS* 3.3 40.3 - - - +
199A ILE 3.3 0.6 - - - -
200A SER* 1.3 75.3 - - - +
202A GLU* 1.3 64.9 + - + +
203A VAL 3.3 0.4 - - - -
204A ASP 3.3 11.7 - - - +
205A PRO* 3.1 40.7 - - + +
207A GLY* 5.8 1.8 - - - +
235A ILE* 5.5 0.2 - - - +
236A PRO* 4.1 33.6 + - - +
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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