Contacts of the helix formed by residues 195 - 207 (chain L) in PDB entry 5DST
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 SER 195 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192L PHE* 2.8 21.0 + - - +
193L TYR 3.0 0.4 - - - -
194L GLU* 1.3 79.5 - - - +
196L MET* 1.3 63.4 + - - +
197L LEU* 3.2 4.6 + - - +
198L ASN* 3.4 35.2 + - - +
199L THR* 4.3 1.6 + - - -
362L PRO* 4.1 13.3 - - - +
367L VAL* 2.8 30.6 + - - -
368L ARG* 4.2 3.7 + - - -
370L LEU* 4.5 6.2 - - - +
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Residues in contact with MET 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L VAL* 3.6 22.4 - - + +
119L GLY* 4.0 3.1 - - - -
184L SER* 3.6 23.8 - - - +
185L GLU 3.9 6.1 - - - +
186L TRP* 3.5 30.6 + - + +
192L PHE 4.5 0.6 + - - -
193L TYR 4.4 2.4 + - - -
194L GLU* 3.1 13.9 + - + +
195L SER* 1.3 74.8 - - - +
197L LEU* 1.3 66.1 + - - +
198L ASN 3.1 0.2 - - - -
199L THR* 3.1 18.2 + - + +
200L VAL* 3.3 9.4 + - + +
368L ARG* 6.1 2.0 - - - +
401L SAH 3.5 60.3 - - + +
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Residues in contact with LEU 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L TRP* 3.8 49.1 - - + -
192L PHE* 4.0 18.6 - - + -
195L SER* 3.2 1.5 - - - -
196L MET* 1.3 78.9 - - - +
198L ASN* 1.3 57.2 + - - +
200L VAL* 2.9 18.2 + - + +
201L ILE* 2.8 42.5 + - + +
278L VAL* 4.2 12.8 - - + -
280L ILE* 4.8 11.7 - - + -
283L VAL* 4.6 5.2 - - + -
288L LEU* 3.7 37.5 - - + -
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Residues in contact with ASN 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L GLU* 5.2 1.3 - - - +
195L SER* 3.4 31.1 + - - +
196L MET 3.1 0.4 - - - -
197L LEU* 1.3 74.3 - - - +
199L THR* 1.3 62.5 + - - +
201L ILE* 3.3 10.1 + - - +
202L PHE* 3.0 21.8 + - - +
285L THR* 4.2 23.8 - - + +
288L LEU* 3.3 23.4 - - - +
362L PRO* 5.1 6.7 - - - +
367L VAL* 4.4 13.3 - - - +
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Residues in contact with THR 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L VAL* 3.8 11.2 - - + -
169L VAL* 3.6 36.6 - - + +
170L GLU* 3.5 16.5 + - - +
195L SER 5.0 0.9 + - - -
196L MET* 3.1 20.2 + - + +
198L ASN* 1.3 75.7 - - - +
200L VAL* 1.3 65.7 + - - +
202L PHE* 3.1 4.0 + - - +
203L ALA* 3.0 21.5 + - - +
368L ARG* 5.3 4.5 + - - -
401L SAH 3.4 28.6 + - + +
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Residues in contact with VAL 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L VAL* 4.1 13.5 - - + -
182L ILE* 4.8 7.0 - - + -
184L SER* 3.6 28.0 - - - +
186L TRP* 3.7 28.7 - - + -
196L MET* 3.3 4.0 + - + +
197L LEU* 2.9 16.2 + - + +
199L THR* 1.3 74.0 - - - +
201L ILE* 1.3 65.1 + - - +
203L ALA* 3.1 5.5 + - - +
204L ARG* 2.8 21.3 + - - +
214L MET* 3.6 27.5 - - + +
280L ILE* 4.4 11.4 - - + -
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Residues in contact with ILE 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L LEU* 2.8 37.6 + - + +
198L ASN* 3.4 9.4 - - - +
200L VAL* 1.3 72.6 - - + +
202L PHE* 1.3 64.2 + - - +
204L ARG* 3.1 29.9 + - - +
205L ASP* 2.9 32.5 + - - +
280L ILE 5.7 0.2 - - - +
283L VAL* 3.2 44.4 - - + +
284L LYS* 4.0 12.1 - - - -
285L THR* 4.1 22.0 - - + +
288L LEU* 4.8 2.9 - - + -
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Residues in contact with PHE 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L VAL* 3.9 14.4 - - + -
170L GLU* 3.6 52.3 - - + +
198L ASN 3.0 13.3 + - - +
199L THR* 3.4 11.0 - - - +
201L ILE* 1.3 76.2 - - - +
203L ALA* 1.3 63.1 + - - +
205L ASP* 3.5 6.3 + - - +
206L LYS* 3.0 59.1 + - + +
207L TRP* 4.6 1.1 - + - -
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Residues in contact with ALA 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 4.1 3.1 - - + -
118L VAL* 3.8 27.4 - - + -
169L VAL* 4.2 5.8 - - + -
182L ILE* 3.9 5.0 - - + +
199L THR 3.0 12.5 + - - +
200L VAL 3.5 7.2 - - - +
202L PHE* 1.3 75.2 - - - +
204L ARG* 1.3 66.2 + - - +
207L TRP* 2.9 54.5 + - + +
208L LEU 3.7 0.3 + - - -
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Residues in contact with ARG 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182L ILE* 3.6 12.6 - - - +
200L VAL 2.8 16.1 + - - +
201L ILE* 3.4 26.9 - - - +
203L ALA* 1.3 71.6 - - - +
205L ASP* 1.3 88.8 + - - +
208L LEU* 2.9 49.1 + - + +
214L MET* 3.9 14.8 - - + -
280L ILE 2.9 27.1 + - - -
281L TYR* 3.1 29.3 + - - +
282L THR* 4.5 2.3 + - - -
283L VAL* 2.9 33.9 + - - +
284L LYS* 4.8 6.1 - - - +
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Residues in contact with ASP 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L LYS* 4.4 6.8 + - - -
201L ILE* 2.9 26.4 + - - +
202L PHE* 3.8 5.8 - - - +
204L ARG* 1.3 110.0 + - - +
206L LYS* 1.3 63.9 + - - +
208L LEU 4.8 2.1 + - - +
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Residues in contact with LYS 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169L VAL 5.5 0.2 + - - -
170L GLU 5.4 2.4 + - - -
171L GLU* 5.8 1.0 - - - +
172L VAL 4.2 3.4 + - - -
173L GLU* 2.9 34.6 + - - -
177L GLU 4.1 2.9 - - - +
178L LYS* 3.1 24.4 + - - +
202L PHE* 3.0 44.9 + - + +
203L ALA 3.9 1.8 - - - +
205L ASP* 1.3 76.6 - - - +
207L TRP* 1.3 96.6 + - + +
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Residues in contact with TRP 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L LEU* 3.6 20.4 - - + -
140L ILE* 4.1 17.9 - - + -
169L VAL* 3.5 42.6 - - + -
172L VAL 3.6 17.9 - - - -
173L GLU* 4.7 1.4 + - - -
174L LEU* 3.4 37.9 - - + +
176L VAL 4.4 4.3 + - - -
177L GLU* 3.6 21.3 - - - -
178L LYS* 3.1 7.2 - - - -
179L VAL* 2.7 42.4 + - + -
182L ILE* 5.4 0.4 - - + -
202L PHE* 4.6 1.1 - + - -
203L ALA* 2.9 28.4 + - + +
206L LYS* 1.3 109.0 - - + +
208L LEU* 1.3 65.9 + - - +
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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