Contacts of the strand formed by residues 191 - 196 (chain M) in PDB entry 6DZT
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 LEU 191 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162M MET* 3.7 25.8 - - + -
181M CYS* 4.0 9.4 - - - -
187M ILE* 3.8 11.7 - - + -
189M SER 3.2 5.1 + - - -
190M TYR* 1.3 75.9 - - - +
192M SER* 1.3 70.7 + - - +
193M TRP* 3.4 35.8 - - + +
206M ILE 4.2 0.3 - - - +
207M TYR* 3.9 0.7 - - - -
208M TYR* 3.4 6.7 + - - +
209M ALA* 2.9 30.1 + - + -
229M PHE* 3.6 46.9 - - + -
246M CYS* 4.3 2.5 - - + -
247M LEU 3.3 11.2 - - - +
249M HIS* 4.9 0.4 - - - -
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Residues in contact with SER 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128M THR* 2.6 34.2 + - - -
191M LEU* 1.3 79.0 + - - +
193M TRP* 1.3 68.5 + - - +
194M TYR* 3.6 19.1 - - - -
204M THR* 5.3 0.4 - - - -
206M ILE 3.2 10.0 + - - -
207M TYR* 4.2 2.6 - - - +
208M TYR 4.9 0.7 + - - -
246M CYS* 3.3 6.6 - - - -
247M LEU 2.8 28.3 + - - -
249M HIS* 3.1 15.0 - - - -
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Residues in contact with TRP 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164M GLN* 3.6 20.2 - - - -
179M ILE* 3.8 18.6 - - + -
180M THR 4.3 1.8 - - - -
181M CYS* 3.6 33.9 - - + -
191M LEU* 3.4 19.6 - - + +
192M SER* 1.3 79.5 - - - +
194M TYR* 1.3 59.3 + - - +
204M THR* 3.8 1.7 - - - +
205M LEU* 2.8 37.7 + - + +
206M ILE* 2.8 39.5 + - + +
209M ALA* 5.3 4.5 + - - -
222M GLY* 5.3 1.6 - - - -
223M SER 5.4 0.2 + - - -
229M PHE* 4.8 2.0 - - - +
230M SER* 4.2 13.3 + - - -
231M LEU* 3.7 51.5 - - + +
244M TYR* 4.7 2.9 - - + -
245M TYR 3.2 25.8 - - - -
246M CYS* 3.6 10.5 - - + -
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Residues in contact with TYR 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67M LEU* 6.1 0.2 - - + -
128M THR* 2.4 26.9 + - - -
129M LEU* 3.1 27.0 + - + +
132M TRP* 3.7 20.9 - + - -
192M SER* 3.6 14.4 - - - -
193M TRP* 1.3 74.8 - - - +
195M GLN* 1.3 60.9 + - - +
196M GLN 4.1 0.2 - - - -
202M PRO* 4.3 13.2 - - + -
203M LYS 3.3 6.7 - - - +
204M THR* 3.4 37.2 - - + -
205M LEU* 4.4 3.1 - - - -
243M THR 3.8 0.3 - - - +
244M TYR* 3.3 9.9 - - - +
245M TYR* 2.9 45.5 + - + +
247M LEU* 3.4 32.2 - - + +
256M PHE* 4.3 13.7 - + + -
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Residues in contact with GLN 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M TYR* 1.3 74.2 - - - +
196M GLN* 1.3 59.9 + - - +
197M LYS* 3.9 25.9 + - + +
201M SER 4.3 0.7 - - - +
202M PRO* 3.4 0.8 - - - +
203M LYS* 2.7 72.7 + - + +
205M LEU* 3.9 15.4 - - + +
220M PHE* 4.1 12.4 - - - -
239M ASP 4.3 8.8 + - - +
240M ASP* 4.6 0.9 - - - +
242M ALA* 3.7 15.6 - - + +
243M THR 3.7 3.6 - - - -
244M TYR* 3.1 35.4 + - + -
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Residues in contact with GLN 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M GLN* 2.8 44.8 + - - +
117M TYR* 3.8 4.6 + - - -
194M TYR 4.1 0.2 - - - -
195M GLN* 1.3 73.5 - - - +
197M LYS* 1.3 75.4 + - - +
198M PRO* 4.3 0.3 - - - +
199M TRP* 5.4 2.2 - - - +
200M LYS 3.4 22.5 + - - +
202M PRO* 3.9 23.8 - - + +
242M ALA* 3.3 3.7 - - - +
243M THR* 3.0 45.4 + - - +
245M TYR* 3.2 23.9 + - + -
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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