Contacts of the helix formed by residues 209 - 220 (chain A) in PDB entry 3H0G
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 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.7 6.5 - - - -
208A LEU* 1.3 104.7 + - - +
210A PRO* 1.3 72.8 - - - +
211A LEU* 4.6 3.6 - - - -
212A GLU* 2.5 49.3 + - - +
213A VAL* 3.1 16.1 + - - +
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Residues in contact with PRO 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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91A PRO* 3.2 33.9 - - + +
92A VAL 4.2 15.9 - - - +
93A PHE* 4.1 27.8 - - + -
209A SER* 1.3 89.4 - - - +
211A LEU* 1.3 73.0 + - + +
212A GLU 3.0 1.8 - - - -
213A VAL* 2.9 17.0 + - + +
214A HIS* 2.9 12.9 + - - +
241A ILE* 3.6 18.7 - - + +
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Residues in contact with LEU 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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91A PRO* 3.5 29.8 - - + +
209A SER* 5.5 1.8 - - - -
210A PRO* 1.3 82.5 - - + +
212A GLU* 1.3 56.8 + - + +
214A HIS* 4.1 9.0 - - + +
215A THR* 2.6 49.7 + - + +
241A ILE* 6.2 0.4 - - - -
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Residues in contact with GLU 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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208A LEU* 3.8 17.3 - - - +
209A SER* 2.5 31.6 + - - +
210A PRO 3.0 0.4 - - - -
211A LEU* 1.3 80.2 - - + +
213A VAL* 1.3 63.7 + - + +
215A THR* 2.3 27.1 + - - -
216A ILE* 3.2 17.5 + - + +
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Residues in contact with VAL 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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101A ILE* 4.3 8.7 - - + -
105A LEU* 6.0 7.6 - - + -
208A LEU* 4.0 15.0 - - + -
209A SER 3.1 20.4 - - - +
210A PRO* 2.9 7.6 + - + +
212A GLU* 1.3 73.9 - - + +
214A HIS* 1.3 66.0 + - - +
216A ILE* 2.9 24.0 + - + +
217A PHE* 2.8 60.3 + - + -
241A ILE* 4.2 7.0 - - + -
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Residues in contact with HIS 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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26A PRO* 5.6 6.8 - - + +
210A PRO 2.9 10.4 + - - +
211A LEU* 4.1 10.5 - - + +
213A VAL* 1.3 74.9 - - - +
215A THR* 1.3 68.0 + - + +
217A PHE* 3.0 7.8 + - - +
218A THR* 2.9 40.9 + - + +
238A ASP* 2.7 51.8 + - + +
241A ILE* 3.2 35.3 - - + +
243A THR* 5.5 6.5 + - - -
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Residues in contact with THR 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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111A ASN* 4.9 3.3 + - - -
211A LEU* 2.6 37.2 - - + +
212A GLU* 2.3 30.3 + - - -
214A HIS* 1.3 79.1 - - + +
216A ILE* 1.3 61.0 + - - +
218A THR* 2.6 19.8 + - - -
219A HIS* 2.5 37.3 - - - -
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Residues in contact with ILE 216 (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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108A VAL* 4.9 4.7 - - + -
109A CYS 4.3 10.5 - - - +
110A TRP* 3.2 30.5 - - + -
111A ASN* 2.5 51.0 - - + +
113A GLY* 4.5 6.4 - - - -
212A GLU* 3.4 20.0 - - + +
213A VAL* 2.9 12.8 + - + +
215A THR* 1.3 81.2 + - - +
217A PHE* 1.3 73.9 + - + +
219A HIS* 3.2 14.0 + - - +
220A ILE* 3.3 10.4 + - - +
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Residues in contact with PHE 217 (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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101A ILE* 2.7 40.2 - - + -
104A ILE* 5.4 11.7 - - + -
105A LEU* 6.4 1.8 - - + -
108A VAL* 5.9 2.5 - - + -
213A VAL* 2.8 45.0 + - + -
214A HIS* 3.0 9.8 + - - +
216A ILE* 1.3 84.2 - - + +
218A THR* 1.3 58.7 + - - +
220A ILE* 2.6 55.0 + - + +
225A LEU* 5.0 3.2 - - - +
237A PRO* 3.8 24.0 - - + -
238A ASP* 4.0 17.3 - - - +
240A MET* 4.6 0.7 - - + -
241A ILE* 4.7 4.7 - - + -
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Residues in contact with THR 218 (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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214A HIS* 2.9 54.9 + - + +
215A THR* 2.6 23.7 + - - -
217A PHE* 1.3 71.5 - - - +
219A HIS* 1.3 66.3 + - - +
220A ILE 3.5 5.5 + - - +
236A ARG* 5.7 3.1 + - - +
238A ASP* 3.8 15.7 - - + +
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Residues in contact with HIS 219 (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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111A ASN* 4.0 25.2 + - - +
112A CYS 5.1 6.4 - - - +
113A GLY 4.9 2.4 - - - +
215A THR* 2.5 39.7 + - - -
216A ILE* 3.2 12.1 + - - +
217A PHE 2.9 1.2 + - - -
218A THR* 1.3 82.8 + - - +
220A ILE* 1.3 70.7 + - - +
221A SER* 3.3 4.9 + - - -
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Residues in contact with ILE 220 (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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108A VAL* 3.6 36.3 - - + -
113A GLY* 4.1 8.9 - - - +
216A ILE 3.3 6.2 + - - +
217A PHE* 2.6 57.0 + - + +
218A THR 3.8 6.1 - - - +
219A HIS* 1.3 75.0 - - - +
221A SER* 1.3 77.9 + - - +
222A SER 3.6 1.0 + - - -
224A ASP* 3.8 13.0 - - + -
225A LEU* 3.6 34.3 - - + +
228A LEU* 6.0 3.8 - - + -
230A LEU* 5.7 0.2 - - + -
237A PRO* 4.6 8.3 - - + -
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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