Contacts of the helix formed by residues 196 - 207 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80H TYR* 6.4 0.4 - - - -
118H VAL* 3.4 34.5 - - + +
119H GLY* 4.0 3.4 - - - +
184H SER* 3.8 10.8 - - - +
185H GLU 4.2 3.4 - - - +
186H TRP* 3.4 34.1 + - + +
192H PHE* 4.6 1.0 + - - +
193H TYR 4.5 1.2 + - - -
194H GLU* 2.9 15.0 + - + +
195H SER* 1.3 72.8 - - - +
197H LEU* 1.3 66.6 + - - +
198H ASN 3.1 3.1 - - - -
199H THR* 2.9 18.7 + - + +
200H VAL* 3.2 8.4 + - + +
368H ARG* 6.1 2.0 - - - +
401H SAH 3.3 60.1 - - + +
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Residues in contact with LEU 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H TRP* 3.8 48.4 - - + +
192H PHE* 3.8 19.1 - - + -
195H SER* 3.2 2.3 - - - -
196H MET* 1.3 78.1 - - - +
198H ASN* 1.3 51.6 + - - +
200H VAL* 2.9 17.9 + - + +
201H ILE* 2.8 47.8 + - + +
278H VAL* 4.2 13.5 - - + -
280H ILE* 4.8 12.6 - - + -
283H VAL* 4.6 4.7 - - + -
288H LEU* 3.8 38.8 - - + -
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Residues in contact with ASN 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170H GLU* 5.1 1.3 - - - +
195H SER* 3.5 28.8 + - - +
197H LEU* 1.3 76.2 - - - +
199H THR* 1.3 59.8 + - - +
201H ILE* 3.4 10.5 - - - +
202H PHE* 3.0 25.8 + - - +
285H THR* 4.2 22.5 - - + +
288H LEU* 3.3 25.3 - - - +
362H PRO* 5.2 6.3 - - - +
367H VAL* 4.5 13.5 - - - +
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Residues in contact with THR 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H VAL* 4.0 9.6 - - + -
169H VAL* 3.6 27.3 - - + +
170H GLU* 3.3 20.6 + - - +
195H SER 5.0 1.0 + - - -
196H MET* 2.9 20.0 + - + -
198H ASN* 1.3 76.7 - - - +
200H VAL* 1.3 65.7 + - - +
202H PHE* 3.3 3.7 + - - +
203H ALA* 3.0 21.5 + - - +
368H ARG* 5.3 4.5 + - - -
401H SAH 3.5 31.4 + - + +
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Residues in contact with VAL 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H VAL* 4.0 10.3 - - + -
182H ILE* 4.8 6.9 - - + +
184H SER* 3.6 28.0 - - - +
186H TRP* 3.8 28.0 - - + -
196H MET* 3.2 4.6 + - + +
197H LEU* 2.9 15.3 + - + +
199H THR* 1.3 76.6 - - - +
201H ILE* 1.3 52.4 + - - +
203H ALA* 3.3 6.2 + - - +
204H ARG* 2.8 33.4 + - - +
214H MET* 3.5 27.5 - - + +
280H ILE* 4.4 11.4 - - + -
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Residues in contact with ILE 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H LEU* 2.8 38.5 + - + +
198H ASN* 3.4 10.3 - - - +
200H VAL* 1.3 70.2 - - - +
202H PHE* 1.3 68.0 + - - +
204H ARG* 3.2 27.3 + - - +
205H ASP* 3.0 32.6 + - - +
283H VAL* 3.2 44.6 - - + +
284H LYS* 3.9 12.6 - - - -
285H THR* 4.0 20.2 - - + +
288H LEU* 4.8 3.1 - - + -
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Residues in contact with PHE 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H VAL* 4.0 17.5 - - + -
170H GLU* 3.7 46.9 - - + +
198H ASN 3.0 10.7 + - - +
199H THR* 3.4 11.4 - - - +
201H ILE* 1.3 80.8 - - - +
203H ALA* 1.3 64.4 + - - +
205H ASP* 3.3 6.2 + - - +
206H LYS* 2.8 59.7 + - + +
207H TRP* 4.6 1.6 - + - -
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Residues in contact with ALA 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 4.2 2.5 - - + -
118H VAL* 3.8 27.4 - - + -
169H VAL* 4.1 5.8 - - + -
182H ILE* 3.9 5.0 - - + +
199H THR 3.0 13.4 + - - +
200H VAL 3.6 4.3 - - - +
202H PHE* 1.3 80.0 - - - +
204H ARG* 1.3 54.0 + - - +
207H TRP* 2.8 65.6 + - + +
208H LEU 3.8 0.5 + - - -
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Residues in contact with ARG 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H ILE* 3.6 11.6 - - - +
200H VAL 2.8 21.5 + - - +
201H ILE* 3.4 23.5 - - - +
203H ALA* 1.3 71.2 - - - +
205H ASP* 1.3 85.1 + - - +
208H LEU* 2.9 53.8 + - + +
214H MET* 3.9 15.5 - - + -
280H ILE 2.8 35.0 + - - -
281H TYR* 3.0 28.9 + - - +
282H THR* 3.6 3.1 + - - -
283H VAL* 2.8 33.9 + - - +
284H LYS* 4.8 5.7 - - - +
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Residues in contact with ASP 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H LYS* 4.4 6.9 + - - -
201H ILE* 3.0 18.9 + - - +
202H PHE* 3.5 10.1 - - - +
204H ARG* 1.3 113.5 + - - +
206H LYS* 1.3 63.6 + - - +
208H LEU 5.0 1.4 + - - +
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Residues in contact with LYS 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H VAL 5.4 0.2 + - - -
170H GLU 5.2 3.4 + - - -
171H GLU 5.7 0.8 - - - -
172H VAL 4.0 8.3 + - - -
173H GLU* 3.0 35.4 + - - -
177H GLU 4.1 3.1 - - - +
178H LYS* 3.2 23.1 + - - +
202H PHE* 2.8 49.1 + - + +
203H ALA 3.8 2.0 - - - +
205H ASP* 1.3 75.1 - - - +
207H TRP* 1.3 92.7 + - + +
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Residues in contact with TRP 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 3.7 19.7 - - + -
140H ILE* 4.1 17.7 - - + -
169H VAL* 3.6 42.2 - - + -
172H VAL 3.7 18.6 - - - -
173H GLU* 4.7 2.0 + - - -
174H LEU* 3.4 42.4 - - + +
176H VAL 4.3 6.5 + - - -
177H GLU 3.5 19.5 - - - -
178H LYS* 3.1 6.4 - - - -
179H VAL* 2.7 40.8 + - + -
182H ILE* 5.4 0.4 - - + -
202H PHE* 4.6 1.6 - + - -
203H ALA* 2.8 33.2 + - + +
206H LYS* 1.3 107.7 - - + +
208H LEU* 1.3 63.2 + - - +
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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