Contacts of the helix formed by residues 207 - 219 (chain B) in PDB entry 4KSL
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 THR 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B MET* 4.4 4.3 - - - +
206B ARG* 1.3 90.8 - - + +
208B ALA* 1.3 64.5 + - - +
209B GLU* 3.7 15.1 + - - +
210B ALA* 3.0 29.0 + - - +
211B ARG* 3.1 20.6 + - - +
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Residues in contact with ALA 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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207B THR* 1.3 74.1 - - - +
209B GLU* 1.3 57.6 + - - +
211B ARG* 3.1 33.2 + - - +
212B GLN* 2.9 41.3 + - - +
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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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207B THR* 3.8 12.7 + - - +
208B ALA* 1.3 79.3 - - - +
210B ALA* 1.3 56.4 + - - +
212B GLN* 3.3 12.7 + - - +
213B ILE* 2.9 52.6 + - + +
348B GLU* 4.7 21.6 - - + +
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Residues in contact with ALA 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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205B MET* 4.0 22.2 - - + +
206B ARG* 5.2 1.6 - - + +
207B THR* 3.0 27.1 + - - +
209B GLU* 1.3 77.3 - - - +
211B ARG* 1.3 58.2 + - - +
213B ILE* 3.9 7.8 - - - +
214B ALA* 2.9 32.4 + - - +
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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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139B MET 4.1 3.1 - - - +
140B SER 2.6 26.5 + - - +
141B GLN* 3.1 31.4 + - - +
142B ALA 3.1 23.5 + - - +
143B VAL* 3.3 24.0 - - - +
202B LEU* 3.4 31.6 - - + +
205B MET* 4.1 12.9 - - + -
207B THR 3.1 12.7 + - - +
208B ALA* 3.4 33.0 + - - +
210B ALA* 1.3 75.8 - - - +
212B GLN* 1.3 70.9 + - - +
215B CYS* 2.9 30.8 + - - +
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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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136B PHE* 5.5 1.2 - - - -
140B SER* 3.9 22.1 + - - +
208B ALA* 2.9 27.4 + - - +
209B GLU* 3.6 14.3 + - - +
211B ARG* 1.3 87.0 - - - +
213B ILE* 1.3 60.4 + - + +
215B CYS* 3.4 6.0 + - - +
216B ASP* 2.9 34.5 + - - +
346B VAL* 3.8 30.8 + - - +
347B CYS 4.0 15.6 - - - +
348B GLU* 4.7 6.6 - - + -
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Residues in contact with ILE 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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209B GLU* 2.9 42.1 + - + +
210B ALA* 3.9 6.5 - - - +
212B GLN* 1.3 76.5 - - + +
214B ALA* 1.3 58.3 + - - +
216B ASP* 3.1 13.5 + - + +
217B GLU* 2.9 32.8 + - + +
348B GLU* 5.5 10.5 - - + -
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Residues in contact with ALA 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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202B LEU* 3.7 15.3 - - + -
205B MET* 3.7 22.7 - - + -
210B ALA 2.9 19.8 + - - +
213B ILE* 1.3 77.8 - - - +
215B CYS* 1.3 57.7 + - - +
217B GLU* 3.0 12.7 + - - +
218B LEU* 2.9 24.6 + - - +
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Residues in contact with CYS 215 (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 PHE* 4.2 6.7 - - + -
139B MET* 4.0 7.2 - - - -
140B SER* 3.7 38.6 - - - -
202B LEU* 3.7 17.4 - - + +
211B ARG 2.9 19.2 + - - +
212B GLN 3.7 4.0 - - - +
214B ALA* 1.3 72.7 - - - +
216B ASP* 1.3 66.5 + - - +
218B LEU* 3.1 10.8 + - - +
219B PHE* 3.0 49.8 - - - -
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Residues in contact with ASP 216 (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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80B LEU* 3.2 30.9 - - + +
121B ARG* 2.9 43.9 + - - -
136B PHE* 3.3 12.8 - - - -
212B GLN* 2.9 16.2 + - - +
213B ILE* 3.2 15.3 - - + +
215B CYS* 1.3 76.4 - - - +
217B GLU* 1.3 62.5 + - + +
218B LEU 3.3 0.5 + - - -
219B PHE* 3.4 6.9 + - - -
220B THR* 3.6 2.3 - - - +
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Residues in contact with GLU 217 (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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213B ILE* 2.9 21.4 + - + +
214B ALA* 3.0 15.9 + - - +
216B ASP* 1.3 77.2 - - + +
218B LEU* 1.3 57.6 + - - +
220B THR* 2.7 39.4 + - - +
221B ASN* 4.4 2.1 - - - +
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Residues in contact with LEU 218 (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 MET* 3.6 31.0 - - + -
198B LYS* 3.8 40.4 - - + +
202B LEU* 4.5 11.0 - - + -
214B ALA 2.9 11.3 + - - +
215B CYS* 3.1 12.5 + - - +
217B GLU* 1.3 78.1 - - - +
219B PHE* 1.3 73.8 + - + +
220B THR 3.3 1.1 + - - -
221B ASN* 3.6 16.7 - - - +
224B GLU* 3.9 16.3 - - + +
225B GLU* 4.7 7.0 + - + +
228B LEU* 4.1 16.8 - - + -
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Residues in contact with PHE 219 (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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80B LEU* 4.4 4.5 - - + -
81B SER* 2.6 41.1 + - - +
82B VAL* 4.6 3.1 - - + -
132B ARG* 4.1 7.6 - - + -
135B LEU* 4.2 6.5 - - + -
136B PHE* 3.4 55.6 - + + -
139B MET* 4.5 9.2 - - - -
215B CYS* 3.0 40.2 + - - +
216B ASP 3.4 5.5 + - - +
217B GLU 3.4 0.6 - - - -
218B LEU* 1.3 91.8 - - + +
220B THR* 1.3 60.8 + - - +
225B GLU* 3.1 31.9 - - + +
228B LEU* 4.9 4.7 - - + -
229B TYR* 3.7 20.0 - + - -
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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