Contacts of the helix formed by residues 207 - 215 (chain A) in PDB entry 4H3E
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A TYR* 4.7 0.2 - - - -
203A ASP 3.7 8.5 + - - -
204A PHE* 3.0 52.2 + - - +
205A GLU* 3.2 9.7 + - - -
206A ASN* 1.3 93.2 - - - +
208A ARG* 1.3 62.5 + - - +
209A PRO* 3.2 7.6 - - + -
210A ASP* 2.7 65.9 + - + +
211A TYR 3.2 9.0 + - - -
214A GLU* 5.0 3.4 + - - -
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Residues in contact with ARG 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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150A GLY 2.9 29.2 + - - -
151A VAL* 3.8 16.7 + - - +
153A ASN 2.7 24.4 + - - -
155A GLY* 3.0 26.3 + - - +
195A VAL* 3.1 27.7 + - + +
197A GLU* 4.7 5.7 + - - +
200A TYR* 3.0 47.1 + - + +
206A ASN 2.8 12.4 + - - +
207A ARG* 1.3 71.9 - - - +
209A PRO* 1.3 69.3 - - + +
211A TYR* 3.2 7.6 + - + +
212A LEU* 2.9 32.1 + - + +
196B TRP* 5.6 2.8 - - - -
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Residues in contact with PRO 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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151A VAL* 3.9 37.0 - - + -
206A ASN 4.4 2.2 - - - +
207A ARG* 3.3 7.6 - - + -
208A ARG* 1.3 94.3 - - + +
210A ASP* 1.3 62.2 + - - +
212A LEU* 3.4 4.1 + - + +
213A LYS* 3.1 47.4 + - - +
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Residues in contact with ASP 210 (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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204A PHE* 3.9 7.2 - - + -
207A ARG* 2.7 54.3 + - - +
209A PRO* 1.3 75.8 - - - +
211A TYR* 1.3 59.7 + - - +
213A LYS* 3.3 13.2 + - - +
214A GLU* 2.9 44.1 + - + +
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Residues in contact with TYR 211 (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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50A VAL* 5.3 0.4 - - + +
51A PHE* 3.6 36.3 - + - -
113A TYR* 2.8 23.3 + - - -
193A VAL* 3.6 21.0 - - + +
194A ASP 2.7 29.6 + - - -
195A VAL* 4.5 2.2 - - + -
199A ALA* 3.8 8.0 - - + +
200A TYR* 3.5 44.4 - + + -
204A PHE* 3.7 22.8 - + + -
207A ARG 3.2 5.9 + - - +
208A ARG* 3.4 11.2 - - + +
210A ASP* 1.3 78.6 - - - +
212A LEU* 1.3 66.4 + - + +
214A GLU* 4.0 0.3 - - - +
215A ILE* 3.0 37.1 + - + +
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Residues in contact with LEU 212 (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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146A PHE* 4.9 11.2 - - + -
147A VAL* 3.8 19.4 - - + +
150A GLY* 3.5 12.6 - - - -
151A VAL* 3.4 43.5 - - + +
193A VAL* 3.6 31.2 - - + -
195A VAL* 4.1 12.3 - - + -
208A ARG* 2.9 25.4 + - + +
209A PRO 3.8 4.0 - - - +
211A TYR* 1.3 82.9 - - + +
213A LYS* 1.3 60.1 + - - +
215A ILE* 3.4 18.5 - - + +
216A TRP* 3.5 15.4 + - - -
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Residues in contact with LYS 213 (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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147A VAL* 4.2 24.5 - - + -
148A GLN* 5.8 1.8 + - - -
209A PRO* 3.1 36.5 + - - +
210A ASP* 3.3 14.3 + - - +
212A LEU* 1.3 75.9 - - - +
214A GLU* 1.3 63.4 + - + +
216A TRP* 3.2 26.3 - - - +
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Residues in contact with GLU 214 (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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49A PRO 5.3 1.0 - - - +
50A VAL* 3.4 20.7 - - + +
204A PHE* 3.3 35.5 - - + -
207A ARG* 5.0 2.9 + - - -
210A ASP* 2.9 24.0 + - - +
211A TYR 4.0 2.0 - - - +
213A LYS* 1.3 76.3 - - + +
215A ILE* 1.3 62.7 + - - +
216A TRP 3.2 2.7 - - - -
217A SER* 2.7 29.4 + - - +
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Residues in contact with ILE 215 (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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50A VAL* 4.5 4.0 - - - +
51A PHE* 3.9 8.3 - - + -
113A TYR* 3.8 32.5 - - + +
117A ILE* 4.2 7.6 - - + -
146A PHE* 6.2 0.7 - - + -
193A VAL* 4.2 24.5 - - + -
211A TYR* 3.0 35.2 + - + +
212A LEU* 3.4 21.3 - - + +
214A GLU* 1.3 74.5 - - - +
216A TRP* 1.3 72.3 + - + +
217A SER 3.1 0.2 - - - -
218A VAL* 2.9 32.1 + - + +
219A ILE* 3.3 18.2 + - + +
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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