Contacts of the helix formed by residues 196 - 207 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D TYR* 6.1 1.1 - - - -
118D VAL* 3.5 35.0 - - + +
119D GLY* 4.0 2.2 - - - -
184D SER* 3.8 11.2 - - - +
185D GLU 4.2 1.1 - - - +
186D TRP* 3.4 35.3 + - + +
192D PHE* 4.7 0.6 + - - +
193D TYR 4.4 2.6 + - - -
194D GLU* 3.1 14.1 + - + +
195D SER* 1.3 72.0 - - - +
197D LEU* 1.3 66.0 + - - +
198D ASN 3.1 2.5 - - - -
199D THR* 3.0 18.4 + - + +
200D VAL* 3.3 7.4 + - - +
368D ARG* 6.1 1.6 - - - +
401D SAH 3.5 60.8 - - + +
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D TRP* 3.7 49.3 - - + +
192D PHE* 3.9 20.6 - - + -
195D SER* 3.3 2.1 - - - -
196D MET* 1.3 77.8 - - - +
198D ASN* 1.3 56.5 + - - +
200D VAL* 3.0 18.1 + - + -
201D ILE* 2.8 41.6 + - + +
278D VAL* 4.2 13.2 - - + -
280D ILE* 4.7 12.3 - - + -
283D VAL* 4.6 4.7 - - + -
288D LEU* 3.7 38.4 - - + -
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Residues in contact with ASN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D GLU* 4.9 1.7 - - - +
195D SER* 3.4 30.5 + - - +
196D MET 3.1 0.4 - - - -
197D LEU* 1.3 75.6 - - - +
199D THR* 1.3 61.5 + - - +
201D ILE* 3.5 10.9 - - - +
202D PHE* 3.1 22.0 + - - +
285D THR* 4.2 22.2 - - + +
288D LEU* 3.3 25.5 - - - +
362D PRO* 5.1 7.1 - - - +
367D VAL* 4.4 12.9 - - - +
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Residues in contact with THR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 3.9 10.1 - - + -
169D VAL* 3.5 37.2 - - + +
170D GLU* 3.3 20.2 + - - +
195D SER 5.0 1.0 + - - -
196D MET* 3.0 20.1 + - + -
198D ASN* 1.3 77.2 - - - +
200D VAL* 1.3 63.2 + - - +
202D PHE* 3.2 4.1 + - - +
203D ALA* 3.0 22.0 + - - +
368D ARG* 5.3 4.5 + - - -
401D SAH 3.4 25.2 + - + +
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Residues in contact with VAL 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 4.1 9.6 - - + -
182D ILE* 4.9 7.0 - - + -
184D SER* 3.5 28.3 - - - +
186D TRP* 3.7 28.5 - - + +
196D MET* 3.3 3.8 + - + +
197D LEU* 3.0 15.7 + - + +
199D THR* 1.3 73.1 - - - +
201D ILE* 1.3 58.3 + - - +
203D ALA* 3.0 7.3 + - - +
204D ARG* 2.7 33.6 + - - +
214D MET* 3.6 27.1 - - + -
280D ILE* 4.3 12.1 - - + -
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D LEU* 2.8 33.5 + - + +
198D ASN* 3.5 11.0 - - - +
200D VAL* 1.3 76.4 - - - +
202D PHE* 1.3 64.5 + - - +
204D ARG* 3.3 25.6 + - - +
205D ASP* 3.0 34.5 + - - +
280D ILE 5.7 0.2 - - - +
283D VAL* 3.1 45.1 - - + +
284D LYS* 3.9 12.3 - - - +
285D THR* 4.1 20.4 - - + +
288D LEU* 4.7 3.4 - - + -
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Residues in contact with PHE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.0 17.0 - - + -
170D GLU* 3.7 46.7 - - + +
198D ASN 3.1 11.3 + - - +
199D THR* 3.4 11.4 - - - +
200D VAL 3.2 0.2 - - - -
201D ILE* 1.3 80.4 - - - +
203D ALA* 1.3 63.0 + - - +
205D ASP* 3.5 5.9 + - - +
206D LYS* 3.0 60.4 + - + +
207D TRP* 4.5 1.6 - + - -
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Residues in contact with ALA 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.1 4.0 - - + -
118D VAL* 3.8 28.0 - - + -
169D VAL* 4.2 5.2 - - + -
182D ILE* 3.8 5.6 - - + +
199D THR 3.0 13.2 + - - +
200D VAL 3.5 5.8 - - - +
202D PHE* 1.3 75.5 - - - +
204D ARG* 1.3 58.3 + - - +
207D TRP* 2.8 62.5 + - + +
208D LEU 3.7 0.5 + - - -
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Residues in contact with ARG 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D ILE* 3.6 12.2 - - - +
200D VAL 2.7 19.5 + - - +
201D ILE* 3.5 22.4 - - - +
203D ALA* 1.3 70.4 - - - +
205D ASP* 1.3 91.6 + - - +
208D LEU* 2.9 51.1 + - + +
214D MET* 3.8 16.6 - - + -
280D ILE 2.8 35.4 + - - -
281D TYR* 3.0 29.4 + - - +
282D THR 4.4 2.7 - - - -
283D VAL* 2.8 35.7 + - - +
284D LYS* 4.8 6.1 - - - +
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Residues in contact with ASP 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D LYS* 4.4 6.8 + - - -
201D ILE* 3.0 24.6 + - - +
202D PHE* 3.7 6.5 - - - +
204D ARG* 1.3 114.9 + - - +
206D LYS* 1.3 62.7 + - - +
208D LEU 4.8 2.3 + - - +
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Residues in contact with LYS 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL 5.5 0.2 + - - -
170D GLU 5.4 2.8 + - - -
171D GLU 5.7 0.6 + - - -
172D VAL 4.1 6.5 + - - -
173D GLU* 2.8 35.0 + - - -
177D GLU 4.0 4.3 - - - +
178D LYS* 3.1 23.4 + - - -
202D PHE* 3.0 45.6 + - + +
203D ALA 4.0 1.6 - - - +
205D ASP* 1.3 77.2 - - - +
207D TRP* 1.3 93.0 + - + +
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Residues in contact with TRP 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 3.7 20.6 - - + -
140D ILE* 4.1 17.0 - - + -
169D VAL* 3.5 41.7 - - + -
172D VAL 3.5 20.4 - - - -
173D GLU* 4.6 2.6 + - - -
174D LEU* 3.3 41.9 - - + +
176D VAL 4.2 8.0 + - - -
177D GLU 3.7 18.8 - - - -
178D LYS* 3.1 7.2 - - - -
179D VAL* 2.7 43.7 + - + -
182D ILE* 5.5 0.2 - - + -
202D PHE* 4.5 1.1 - + - -
203D ALA* 2.8 31.8 + - + +
206D LYS* 1.3 108.5 - - + +
208D LEU* 1.3 58.5 + - - +
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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