Contacts of the helix formed by residues 203 - 212 (chain B) in PDB entry 5FFO
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 ALA 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B SER* 3.2 32.3 + - - +
153B PHE* 4.2 17.9 - - + -
155B LEU* 4.2 7.4 - - + -
201B ASN 2.8 10.6 + - - +
202B ASP* 1.3 70.6 - - - +
204B GLU* 1.3 67.0 + - + +
205B ARG 3.2 1.6 - - - -
206B PHE* 3.3 14.1 + - - +
207B ASN* 3.4 4.7 + - - -
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Residues in contact with GLU 204 (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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203B ALA* 1.3 76.1 - - + +
205B ARG* 1.3 63.9 + - - +
206B PHE 3.2 0.4 - - - -
207B ASN* 3.5 14.6 + - + +
208B GLU* 3.2 40.3 + - + +
211B LYS* 5.2 0.2 + - - -
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Residues in contact with ARG 205 (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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197B LEU* 4.5 18.4 - - + -
200B THR* 5.8 0.4 - - - +
202B ASP* 3.9 24.0 + - + +
203B ALA 3.2 0.6 - - - -
204B GLU* 1.3 77.9 - - - +
206B PHE* 1.3 62.8 + - - +
208B GLU* 3.6 20.0 + - - +
209B ILE* 3.2 37.0 + - + +
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Residues in contact with PHE 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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120B TYR* 3.8 25.1 - + + -
139B GLY* 3.4 34.5 - - - -
142B LEU* 4.5 4.9 - - + -
143B SER* 3.9 3.6 - - - -
155B LEU* 3.5 41.1 - - + -
156B GLY 3.5 24.7 - - - -
157B PHE* 4.1 9.0 - - + -
197B LEU* 3.7 21.2 - - + +
202B ASP 3.9 2.2 + - - +
203B ALA 3.3 10.4 + - - +
204B GLU 3.2 0.2 - - - -
205B ARG* 1.3 79.6 - - - +
207B ASN* 1.3 75.8 + - - +
209B ILE* 3.2 13.3 + - - +
210B VAL* 3.4 29.9 + - + +
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Residues in contact with ASN 207 (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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139B GLY 3.8 0.2 - - - -
140B SER* 3.4 26.3 + - - +
143B SER* 3.2 35.5 + - - -
203B ALA 3.4 9.1 + - - -
204B GLU* 3.5 17.1 + - - +
205B ARG 3.4 0.4 - - - -
206B PHE* 1.3 82.6 - - - +
208B GLU* 1.3 62.4 + - - +
209B ILE 3.0 1.4 + - - -
210B VAL* 3.1 16.4 + - - +
211B LYS* 3.1 38.5 + - - +
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Residues in contact with GLU 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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204B GLU* 3.2 32.1 + - - +
205B ARG* 3.8 24.3 + - - +
206B PHE 3.3 0.4 - - - -
207B ASN* 1.3 76.2 - - - +
209B ILE* 1.3 58.1 + - + +
211B LYS* 3.9 22.0 - - + +
212B ASN* 3.1 31.5 + - - +
41D PRO 5.5 4.0 - - - +
42D GLY* 5.9 3.6 - - - -
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Residues in contact with ILE 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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157B PHE* 3.7 20.9 - - + -
196B ILE* 3.9 17.5 - - + +
197B LEU* 3.6 41.1 - - + -
205B ARG* 3.2 29.4 - - + +
206B PHE 3.2 6.0 + - - +
207B ASN 3.0 1.0 - - - -
208B GLU* 1.3 78.8 - - + +
210B VAL* 1.3 65.7 + - + +
211B LYS 3.2 0.7 + - - -
212B ASN* 3.4 10.4 + - - +
213B GLN* 3.2 37.3 + - - +
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Residues in contact with VAL 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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120B TYR* 5.1 1.8 - - + -
122B MET* 3.8 18.6 - - + -
135B ILE* 4.0 7.9 - - + +
136B LYS* 3.2 51.4 - - + +
139B GLY* 4.9 4.3 - - - -
157B PHE* 4.7 12.3 - - + -
206B PHE* 3.4 44.4 - - + +
207B ASN* 3.1 7.0 + - - +
209B ILE* 1.3 75.5 - - + +
211B LYS* 1.3 63.5 + - + +
213B GLN* 3.4 16.0 + - - +
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Residues in contact with LYS 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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136B LYS* 2.8 36.0 + - + -
140B SER* 6.0 3.1 - - - -
204B GLU 5.2 0.2 + - - -
207B ASN* 3.1 37.8 + - - +
208B GLU* 3.9 21.7 - - + +
209B ILE 3.2 0.4 - - - -
210B VAL* 1.3 79.0 - - + +
212B ASN* 1.3 67.2 + - - +
213B GLN 3.2 0.2 - - - -
40D PRO* 5.9 1.4 - - - +
41D PRO 4.2 6.1 + - - -
42D GLY* 4.5 1.8 - - - -
43D PRO* 3.6 55.5 - - + +
44D LEU 5.3 6.3 + - - +
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Residues in contact with ASN 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 GLU* 3.1 22.2 + - - +
209B ILE* 3.4 6.1 + - - +
210B VAL 3.3 0.6 - - - -
211B LYS* 1.3 83.5 - - - +
213B GLN* 1.3 64.3 + - - +
214B LYS* 3.3 22.6 + - - +
42D GLY 4.8 8.0 - - - +
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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