Contacts of the strand formed by residues 196 - 204 (chain M) in PDB entry 3SDI
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 GLY 196 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38M ASP 4.6 8.7 - - - -
190M ILE 3.6 1.6 - - - +
191M ILE* 3.5 3.1 - - - -
192M ASP* 2.7 45.1 + - - +
194M ASN 3.2 3.8 + - - -
195M THR* 1.3 79.1 - - - +
197M LEU* 1.3 59.3 + - - -
198M THR* 4.0 1.0 + - - -
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Residues in contact with LEU 197 (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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35M PRO* 4.2 15.0 - - + -
37M GLY 4.4 4.7 - - - +
38M ASP* 3.8 31.2 + - + +
39M ASN 4.5 0.7 - - - +
40M THR 4.2 10.1 - - - +
41M VAL* 4.0 26.2 - - + -
189M ALA* 5.7 0.7 - - + -
190M ILE 3.5 7.2 - - - +
191M ILE* 4.5 9.2 - - + +
195M THR 3.6 3.7 + - - +
196M GLY* 1.3 72.9 - - - -
198M THR* 1.3 64.3 + - - +
199M PHE* 4.2 20.1 + - + +
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Residues in contact with THR 198 (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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189M ALA* 3.3 3.6 - - - +
190M ILE* 2.9 54.1 + - + +
192M ASP* 6.1 0.2 - - - +
195M THR* 4.7 17.0 + - - +
196M GLY 4.7 2.3 + - - -
197M LEU* 1.3 74.8 - - - +
199M PHE* 1.3 62.6 + - - +
200M LYS* 4.0 23.6 + - + +
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Residues in contact with PHE 199 (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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31M GLU* 3.5 41.5 - - + -
33M LEU* 3.7 29.4 - - + -
35M PRO* 4.0 29.4 - - + -
41M VAL* 4.9 3.1 - - + -
187M SER* 4.5 4.9 - - - -
188M LEU 3.8 2.0 - - - -
189M ALA* 3.9 17.5 - - + -
197M LEU* 4.1 14.8 + - + +
198M THR* 1.3 75.7 - - - +
200M LYS* 1.3 62.5 + - - +
201M LYS* 3.6 30.5 + - + +
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Residues in contact with LYS 200 (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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165M GLU* 2.6 39.1 + - - +
187M SER* 3.4 6.9 - - - -
188M LEU* 2.7 46.0 + - + +
190M ILE* 4.2 18.2 - - - +
198M THR* 4.5 20.2 - - + +
199M PHE* 1.3 75.3 - - - +
201M LYS* 1.3 60.7 + - - +
203M LEU* 3.8 27.8 - - + +
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Residues in contact with LYS 201 (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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31M GLU* 3.3 32.0 + - - +
186M PHE 4.5 0.2 - - - -
187M SER* 4.4 4.0 - - - +
199M PHE* 3.6 31.8 + - + +
200M LYS* 1.3 73.0 - - - +
202M ASN* 1.3 83.5 + - - +
203M LEU* 3.2 13.4 + - - +
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Residues in contact with ASN 202 (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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17M ASN* 4.9 13.1 - - - +
185M ASN* 5.0 5.4 - - - +
186M PHE 3.9 6.1 + - - -
187M SER* 4.8 2.4 + - - -
201M LYS* 1.3 85.0 - - - +
203M LEU* 1.3 63.4 + - - +
204M GLN* 3.9 6.4 + - - +
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Residues in contact with LEU 203 (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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165M GLU* 5.3 2.2 - - - +
169M VAL* 5.5 2.9 - - + -
185M ASN* 3.1 8.1 - - - +
186M PHE* 3.0 56.8 + - + +
188M LEU* 3.8 33.0 - - + +
200M LYS* 3.8 34.5 - - + +
201M LYS 3.2 17.9 + - - +
202M ASN* 1.3 77.9 - - - +
204M GLN* 1.3 60.6 + - - +
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Residues in contact with GLN 204 (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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1872 GLN* 5.6 2.7 + - - -
169M VAL* 5.6 3.6 - - - +
184M ARG* 3.7 28.9 + - + +
185M ASN* 3.6 27.2 + - + +
186M PHE* 3.9 9.5 - - - -
202M ASN 3.9 6.9 + - - +
203M LEU* 1.3 79.1 - - - +
205M VAL* 1.3 64.4 + - - +
206M GLU* 3.2 33.9 + - + +
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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