Contacts of the helix formed by residues 205 - 214 (chain B) in PDB entry 5W4A
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 LYS 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 5.5 3.4 + - - +
12B LEU* 3.6 30.2 - - + +
14B ILE* 6.1 0.2 - - + -
27B VAL* 4.3 18.1 + - + +
30B ASP* 3.2 41.7 + - + +
201B LEU* 2.7 33.0 + - + +
204B THR* 1.3 84.6 + - - +
206B PRO* 1.3 66.1 - - - +
207B LYS 3.2 2.7 - - - -
208B LEU* 3.1 30.1 + - + +
209B ALA* 3.1 9.4 + - - +
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Residues in contact with PRO 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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70A ASP* 4.2 16.2 - - - +
201B LEU 3.8 0.4 - - - -
202B ASP* 3.7 24.5 - - + +
203B GLN 5.2 0.2 - - - -
204B THR 3.7 7.0 - - - +
205B LYS* 1.3 89.4 - - - +
207B LYS* 1.3 75.0 + - + +
209B ALA* 3.3 8.7 + - + +
210B ASP* 2.9 28.8 + - - +
213B ARG* 5.5 0.2 + - - -
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Residues in contact with LYS 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 6.1 0.9 - - - +
34B VAL* 3.9 30.1 - - + -
205B LYS 3.2 1.2 - - - -
206B PRO* 1.3 88.7 - - + +
208B LEU* 1.3 64.9 + - - +
210B ASP* 3.4 9.8 + - + +
211B ILE* 3.2 27.6 + - + +
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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
----------------------------------------------------------
14B ILE* 5.6 0.9 - - + -
26B ALA* 4.0 15.7 - - + +
30B ASP* 3.9 24.0 - - + -
33B LEU* 3.7 31.0 - - + -
34B VAL* 3.8 18.8 - - + -
48B PHE* 3.8 31.3 - - + +
201B LEU* 4.0 10.8 - - + -
205B LYS* 3.1 27.7 + - + +
207B LYS* 1.3 76.3 - - - +
209B ALA* 1.3 66.4 - - - +
211B ILE* 3.2 8.9 + - + +
212B ILE* 3.1 24.4 + - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 3.8 24.6 - - + +
201B LEU* 3.7 8.2 - - + +
202B ASP* 3.1 33.4 - - - +
205B LYS 3.1 11.9 + - - +
206B PRO* 3.6 7.6 - - + +
208B LEU* 1.3 77.0 - - - +
210B ASP* 1.3 56.6 + - - +
212B ILE* 3.3 4.2 + - - +
213B ARG* 3.0 34.5 + - - +
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Residues in contact with ASP 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 PRO 2.9 17.8 + - - +
207B LYS* 3.7 12.3 - - + +
208B LEU 3.2 0.4 - - - -
209B ALA* 1.3 76.7 - - - +
211B ILE* 1.3 58.4 + - + +
213B ARG* 3.3 13.1 + - - +
214B ASN* 2.8 54.7 + - - +
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Residues in contact with ILE 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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33B LEU 3.9 7.9 - - - +
34B VAL* 3.8 40.8 - - + +
48B PHE 3.2 16.4 - - - +
49B GLY* 3.4 24.6 - - - +
50B ALA* 3.6 9.6 - - + +
207B LYS* 3.2 18.3 + - + +
208B LEU* 3.2 9.8 + - + +
210B ASP* 1.3 74.6 - - + +
212B ILE* 1.3 66.6 + - - +
214B ASN 3.9 4.9 - - - +
215B GLY* 3.2 28.0 + - - +
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Residues in contact with ILE 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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47B VAL* 4.3 6.7 - - + +
48B PHE* 3.5 43.5 - - + +
49B GLY* 4.7 2.5 - - - -
173B TYR* 3.8 25.4 + - + +
194B ARG* 4.1 20.7 + - + -
197B PHE* 3.8 31.0 - - + -
198B LEU* 3.8 21.1 - - + -
201B LEU* 4.0 6.1 - - + -
208B LEU 3.1 11.0 + - - +
209B ALA 3.3 7.4 + - - +
211B ILE* 1.3 77.9 - - - +
213B ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 213 (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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194B ARG* 5.6 3.4 - - - +
195B ASP* 5.2 5.5 + - - +
198B LEU* 3.7 34.9 - - + +
199B ASN* 5.1 3.8 + - - -
202B ASP* 2.9 41.4 + - - -
206B PRO 5.5 0.2 + - - -
209B ALA* 3.0 25.8 + - - +
210B ASP* 3.6 15.8 + - - +
211B ILE 3.2 0.2 - - - -
212B ILE* 1.3 79.4 - - - +
214B ASN* 1.3 78.5 + - - +
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Residues in contact with ASN 214 (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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210B ASP* 2.8 42.7 + - - +
211B ILE* 3.4 6.2 + - - +
213B ARG* 1.3 91.8 + - - +
215B GLY* 1.3 58.1 + - - +
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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