Contacts of the helix formed by residues 196 - 207 (chain O) 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 MET 196 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80O TYR* 6.1 0.7 - - - -
118O VAL* 3.5 33.9 - - + +
119O GLY* 3.9 5.6 - - - -
184O SER* 3.8 11.0 - - - +
185O GLU 4.1 6.7 - - - +
186O TRP* 3.3 32.8 + - + +
192O PHE 4.6 0.8 + - - -
193O TYR 4.5 1.4 + - - -
194O GLU* 3.0 13.2 + - + +
195O SER* 1.3 72.0 - - - +
197O LEU* 1.3 64.6 + - - +
198O ASN 3.2 2.5 - - - -
199O THR* 3.0 18.5 + - - +
200O VAL* 3.2 8.7 + - - +
368O ARG* 6.0 2.5 - - - +
401O SAH 3.4 59.9 - - + +
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Residues in contact with LEU 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186O TRP* 3.8 48.0 - - + +
192O PHE* 3.8 20.0 - - + -
195O SER* 3.3 1.7 - - - -
196O MET* 1.3 76.9 - - - +
198O ASN* 1.3 51.0 + - - +
200O VAL* 2.8 21.9 + - + +
201O ILE* 2.8 47.4 + - + +
278O VAL* 4.2 13.7 - - + -
280O ILE* 4.8 12.6 - - + -
283O VAL* 4.7 4.0 - - + -
288O LEU* 3.7 38.8 - - + -
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Residues in contact with ASN 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170O GLU* 5.2 0.7 - - - -
195O SER* 3.3 32.4 + - - +
196O MET 3.2 0.2 - - - -
197O LEU* 1.3 74.3 - - - +
199O THR* 1.3 57.3 + - - +
201O ILE* 3.3 11.3 - - - +
202O PHE* 3.0 27.0 + - - +
285O THR* 4.2 23.6 - - + +
288O LEU* 3.3 23.6 - - - +
362O PRO* 5.1 7.1 - - - +
367O VAL* 4.4 12.7 - - - +
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Residues in contact with THR 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O VAL* 4.0 9.9 - - + -
169O VAL* 3.6 36.8 - - + +
170O GLU* 3.1 25.2 + - - +
195O SER 5.1 0.9 + - - -
196O MET* 3.0 20.0 + - + -
198O ASN* 1.3 75.3 - - - +
200O VAL* 1.3 66.0 + - - +
202O PHE* 3.4 2.9 + - - +
203O ALA* 3.0 22.0 + - - +
368O ARG* 5.4 3.6 + - - -
401O SAH 3.6 19.3 + - + +
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Residues in contact with VAL 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O VAL* 4.1 10.8 - - + -
182O ILE* 4.8 7.2 - - + -
184O SER* 3.5 27.1 - - - +
186O TRP* 3.6 28.3 - - + -
196O MET* 3.2 4.4 + - + +
197O LEU* 2.8 15.7 + - + +
199O THR* 1.3 72.9 - - - +
201O ILE* 1.3 61.6 + - - +
203O ALA* 3.2 7.2 + - - +
204O ARG* 2.8 28.6 + - - +
214O MET* 3.5 28.0 - - + -
280O ILE* 4.4 11.7 - - + -
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Residues in contact with ILE 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197O LEU* 2.8 37.6 + - + +
198O ASN* 3.3 10.8 - - - +
200O VAL* 1.3 72.4 - - - +
202O PHE* 1.3 65.1 + - - +
204O ARG* 3.1 28.1 + - - +
205O ASP* 2.9 33.6 + - - +
283O VAL* 3.1 45.8 - - + +
284O LYS* 4.0 12.1 - - - -
285O THR* 4.0 19.7 - - + +
288O LEU* 4.7 3.4 - - + -
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Residues in contact with PHE 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169O VAL* 3.8 13.9 - - + -
170O GLU* 3.6 50.7 - - + +
198O ASN 3.0 13.8 + - - +
199O THR* 3.5 11.2 - - - +
201O ILE* 1.3 78.1 - - - +
203O ALA* 1.3 67.5 + - - +
205O ASP* 3.8 5.5 - - - +
206O LYS* 3.1 55.3 + - + +
207O TRP* 4.5 1.1 - + - -
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Residues in contact with ALA 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU* 4.1 2.9 - - + -
118O VAL* 3.9 26.7 - - + -
169O VAL* 4.2 4.5 - - + -
182O ILE* 3.9 4.8 - - + +
199O THR 3.0 11.7 + - - +
200O VAL 3.5 7.4 - - - +
202O PHE* 1.3 76.7 - - - +
204O ARG* 1.3 67.1 + - - +
207O TRP* 2.8 55.7 + - + +
208O LEU 3.7 0.5 + - - -
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Residues in contact with ARG 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O ILE* 3.5 13.1 - - - +
200O VAL 2.8 19.7 + - - +
201O ILE* 3.4 23.7 - - - +
203O ALA* 1.3 69.5 - - - +
205O ASP* 1.3 89.7 + - - +
208O LEU* 2.8 54.2 + - + +
214O MET* 3.9 16.6 - - + -
280O ILE 2.8 34.4 + - - -
281O TYR* 3.0 29.0 + - - +
282O THR* 3.4 4.2 + - - +
283O VAL* 2.9 32.5 + - - +
284O LYS* 4.9 5.5 - - - +
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Residues in contact with ASP 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O LYS* 4.5 5.7 + - - -
201O ILE* 2.9 26.6 + - - +
202O PHE* 3.8 5.8 + - - +
204O ARG* 1.3 111.6 + - - +
206O LYS* 1.3 63.6 + - - +
208O LEU 4.8 2.4 + - - +
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Residues in contact with LYS 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169O VAL 5.4 0.2 + - - -
170O GLU 5.4 2.8 + - - -
171O GLU 5.5 1.0 + - - -
172O VAL 4.1 6.9 + - - -
173O GLU* 3.0 34.6 + - - -
177O GLU 4.2 2.6 - - - +
178O LYS* 3.1 26.5 + - - +
202O PHE* 3.1 44.4 + - + +
203O ALA 3.9 1.8 - - - +
205O ASP* 1.3 76.7 - - - +
207O TRP* 1.3 94.5 + - + +
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Residues in contact with TRP 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU* 3.6 20.0 - - + -
140O ILE* 4.0 18.2 - - + -
169O VAL* 3.4 41.7 - - + -
172O VAL 3.5 19.7 - - - -
173O GLU* 4.7 2.7 + - - -
174O LEU* 3.4 35.2 - - + +
176O VAL 4.4 7.0 + - - -
177O GLU 3.6 19.5 - - - -
178O LYS* 3.1 7.0 - - - -
179O VAL* 2.6 47.5 + - + -
182O ILE* 5.4 0.4 - - + -
202O PHE* 4.5 0.9 - + - -
203O ALA* 2.8 32.4 + - + +
206O LYS* 1.3 110.1 - - + +
208O LEU* 1.3 58.4 + - - +
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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