Contacts of the helix formed by residues 204 - 212 (chain B) in PDB entry 4U7C
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 ILE 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B THR* 3.1 31.3 + - + +
104B VAL* 3.6 24.2 - - + -
188B TYR* 4.2 22.9 - - + +
202B LEU* 3.9 24.0 - - + -
203B ASN* 1.3 72.6 - - - +
205B THR* 1.3 58.8 + - - +
206B LYS 3.5 0.9 - - - -
207B HIS* 3.9 16.4 - - + +
208B LEU* 3.0 36.2 + - + +
290B ALA* 4.4 8.1 - - + +
293B VAL* 4.0 26.7 - - + -
294B VAL* 4.8 0.7 - - + -
297B ILE* 5.2 1.8 - - + -
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B SER 4.4 12.6 - - - +
101B ASN* 3.4 12.1 - - - +
102B THR* 2.9 30.8 + - - +
203B ASN* 3.0 17.5 + - - -
204B ILE* 1.3 75.1 - - - +
206B LYS* 1.3 68.9 + - + +
208B LEU* 3.2 5.9 + - - +
209B GLU* 2.9 36.5 + - + +
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR 5.7 1.8 - - - +
203B ASN 4.6 5.0 + - - +
205B THR* 1.3 77.5 - - + +
207B HIS* 1.3 58.0 - - - +
209B GLU* 3.1 23.3 + - - +
210B GLU* 2.5 69.6 + - - +
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Residues in contact with HIS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP 4.4 5.3 + - - +
188B TYR* 3.4 58.9 + + + +
204B ILE* 3.7 11.1 + - + +
205B THR 3.2 0.6 - - - -
206B LYS* 1.3 77.6 - - - +
208B LEU* 1.3 61.2 + - - +
210B GLU* 3.3 8.1 + - - +
211B ARG* 2.9 64.8 + - + +
214B TRP* 3.8 27.1 - + - -
293B VAL* 3.7 21.8 - - + +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR* 3.5 28.0 - - + +
204B ILE* 3.0 28.1 + - + +
205B THR* 3.2 5.1 + - - +
207B HIS* 1.3 74.7 - - - +
209B GLU* 1.3 64.3 + - - +
211B ARG* 3.0 13.7 + - - +
212B GLN* 3.0 22.5 + - - +
288B THR 3.4 24.9 - - - +
289B SER* 4.4 0.2 - - - -
290B ALA* 3.6 28.9 - - + +
293B VAL* 3.6 23.3 - - + -
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B THR* 2.9 25.5 + - + +
206B LYS* 3.1 32.0 + - - +
208B LEU* 1.3 78.4 - - - +
210B GLU* 1.3 63.9 + - + +
211B ARG 3.2 0.3 + - - -
212B GLN* 3.3 22.4 + - - +
213B ASN* 4.1 5.4 - - - +
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B LYS* 2.5 50.0 + - - +
207B HIS* 3.6 5.6 - - - +
209B GLU* 1.3 81.9 - - + +
211B ARG* 1.3 58.1 + - - +
212B GLN 3.3 0.4 - - - -
213B ASN* 3.6 15.4 + - - +
214B TRP* 2.9 36.6 + - + +
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 4.4 1.0 - - - -
207B HIS* 2.9 46.0 + - + +
208B LEU* 3.0 6.2 + - - +
210B GLU* 1.3 75.5 - - - +
212B GLN* 1.3 66.2 + - - +
213B ASN 3.2 2.6 + - - -
214B TRP* 3.5 36.4 + - + +
219B ARG* 3.7 17.7 - - - +
286B PHE* 3.7 8.1 - - - +
287B GLY 2.7 29.7 + - - -
288B THR* 3.1 25.7 - - + +
293B VAL* 3.5 30.1 - - - +
296B GLU* 2.6 43.0 + - - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.0 19.4 + - - +
209B GLU* 3.3 16.9 + - - +
211B ARG* 1.3 80.5 - - - +
213B ASN* 1.3 60.8 + - + +
214B TRP 3.6 2.6 + - - -
288B THR* 4.1 26.5 + - - +
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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