Contacts of the helix formed by residues 207 - 216 (chain A) in PDB entry 3U78
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 LEU 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A VAL* 4.1 8.3 - - + +
183A GLU* 3.7 29.4 - - - -
186A VAL* 3.7 33.0 - - + -
187A GLY 3.9 8.5 - - - +
188A GLY* 3.4 6.5 + - - +
190A LYS* 2.8 18.5 + - + +
192A ILE* 3.8 29.9 - - + +
205A MET 3.7 0.8 + - - -
206A THR* 1.3 70.7 - - - +
208A HIS* 1.3 61.6 + - - +
210A TYR* 3.3 2.3 + - + -
211A VAL* 3.0 37.8 + - + +
228A LEU* 4.2 9.0 - - + -
272A MET* 4.2 19.5 - - + -
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Residues in contact with HIS 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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180A MET* 6.0 4.0 - - + -
183A GLU* 2.6 36.2 + - - +
188A GLY 2.9 20.7 + - - +
189A ASP* 5.8 0.9 - - - +
206A THR* 3.5 5.2 - - + +
207A LEU* 1.3 77.6 - - - +
209A ASN* 1.3 77.8 + - - +
211A VAL* 3.4 5.9 + - - +
212A LYS* 3.1 39.6 + - + +
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Residues in contact with ASN 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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205A MET* 3.2 20.4 - - + +
206A THR* 2.7 35.4 + - - +
208A HIS* 1.3 80.7 - - - +
210A TYR* 1.3 66.5 + - - +
211A VAL 3.0 1.6 - - - -
212A LYS* 2.8 33.4 + - - +
213A TYR* 2.7 23.6 + - - +
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Residues in contact with TYR 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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179A VAL* 5.6 0.2 - - + -
192A ILE* 4.1 13.2 - - + -
194A VAL* 4.1 13.7 - - + -
205A MET* 3.0 23.6 - - + +
206A THR 3.1 8.9 + - - +
207A LEU 3.3 6.5 + - - +
209A ASN* 1.3 74.2 - - - +
211A VAL* 1.3 56.5 + - + +
213A TYR* 3.3 11.0 + + - +
214A PHE* 2.7 71.0 + + + +
223A LEU* 2.7 42.4 + - + -
225A VAL* 3.6 31.6 - - + -
272A MET* 3.5 35.1 + - + -
273A GLY* 3.7 4.2 - - - -
274A VAL* 4.0 0.9 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.2 44.0 - - + +
180A MET* 3.7 29.8 - - + -
183A GLU* 3.9 17.0 - - + +
207A LEU* 3.0 25.8 + - + +
208A HIS 3.5 7.9 - - - +
209A ASN 3.0 0.4 - - - -
210A TYR* 1.3 75.7 - - + +
212A LYS* 1.3 55.6 + - + +
214A PHE* 3.6 0.8 - - - +
215A MET* 2.7 41.3 + - + +
272A MET* 5.5 0.7 - - - -
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Residues in contact with LYS 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 HIS* 3.1 34.4 + - + +
209A ASN* 2.8 36.5 + - - +
211A VAL* 1.3 74.6 - - + +
213A TYR* 1.3 64.4 + - - +
215A MET* 3.1 4.6 + - - +
216A ASN* 3.1 26.5 + - - +
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Residues in contact with TYR 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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205A MET* 4.4 7.6 - - + -
209A ASN 2.7 15.0 + - - +
210A TYR* 3.4 27.6 - + - +
212A LYS* 1.3 74.8 - - - +
214A PHE* 1.3 66.1 + - - +
216A ASN* 3.3 17.2 + - - +
219A ARG* 3.7 23.6 - - + +
220A PRO* 4.5 11.7 - - + -
221A LYS* 2.5 34.9 + - + -
223A LEU* 2.8 47.5 + - + -
274A VAL* 3.4 33.3 - - + +
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Residues in contact with PHE 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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179A VAL* 3.8 29.6 - - + -
210A TYR* 2.7 47.9 + + + +
211A VAL* 3.6 8.5 - - - +
213A TYR* 1.3 79.4 - - - +
215A MET* 1.3 71.5 + - - +
216A ASN 3.2 5.9 + - - +
219A ARG* 3.2 31.6 + - - +
272A MET* 4.5 0.9 - - + -
273A GLY 3.9 21.1 - - - -
274A VAL* 3.7 20.4 - - + -
296A TRP* 4.1 25.4 - + - -
361A ASP* 4.1 18.8 - - + -
362A CYS 4.8 0.9 - - - -
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Residues in contact with MET 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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178A SER* 6.2 2.9 - - - -
179A VAL* 4.8 9.0 - - + -
180A MET* 5.4 12.3 - - + -
211A VAL* 2.7 37.5 + - + +
212A LYS* 3.1 4.9 + - - +
214A PHE* 1.3 84.2 - - - +
216A ASN* 1.3 59.8 + - - +
217A PRO* 3.6 7.8 - - - +
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Residues in contact with ASN 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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212A LYS 3.1 15.3 + - - +
213A TYR* 3.3 16.3 - - - +
214A PHE 3.3 6.3 - - - +
215A MET* 1.3 77.3 - - - +
217A PRO* 1.3 99.2 + - - +
218A ASN* 4.1 16.6 + - - +
219A ARG* 3.6 9.3 + - - +
220A PRO* 6.0 0.6 - - - +
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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