Contacts of the strand formed by residues 196 - 201 (chain B) in PDB entry 3UAJ
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 4.8 2.6 - - - +
130B VAL* 3.4 18.4 + - + +
191B ILE* 3.8 37.2 - - + -
192B ASP 3.3 17.9 - - - +
193B PHE* 3.2 19.2 + - + +
194B ASN 3.5 0.9 - - - -
195B GLU* 1.4 87.8 - - + +
197B ILE* 1.3 72.0 + - - +
207B LEU* 4.4 24.2 - - + +
208B VAL* 3.4 26.9 - - - +
209B HIS* 3.9 15.0 - - + +
210B LYS* 4.4 1.4 - - - +
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.8 23.6 - - + -
127B GLY* 4.3 11.0 - - - -
128B ASN 3.9 5.6 - - - +
129B LEU* 3.8 36.3 - - + +
130B VAL* 4.4 3.1 - - - -
196B MET* 1.3 81.0 - - - +
198B LEU* 1.3 66.6 + - - +
199B MET 3.3 6.4 + - - +
206B TRP 3.7 0.2 - - - +
207B LEU* 3.8 2.5 - - - -
208B VAL* 2.7 39.0 + - + +
209B HIS 4.4 5.4 - - - +
210B LYS* 3.8 28.0 - - + +
213B PHE* 4.0 28.9 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 4.7 15.0 - - + +
53B VAL* 4.8 13.2 - - + -
127B GLY* 3.6 0.5 - - - -
128B ASN* 2.8 50.9 + - + +
130B VAL* 3.6 22.8 - - + +
197B ILE* 1.3 67.7 - - - +
199B MET* 1.3 59.1 + - - +
200B LYS* 3.9 1.4 + - - +
205B THR* 3.8 19.8 - - + +
206B TRP 3.5 3.6 - - - +
207B LEU* 4.0 7.0 - - + -
270B VAL* 3.8 18.8 - - + -
279B PHE* 3.7 32.8 - - + -
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ILE* 3.7 30.7 - - + -
126B THR 3.4 14.6 - - - +
127B GLY* 4.1 1.3 - - - -
197B ILE* 3.3 2.3 + - + -
198B LEU* 1.3 72.0 - - - +
200B LYS* 1.3 56.2 + - - +
201B MET* 4.8 0.4 - - + -
205B THR* 3.4 1.5 - - - -
206B TRP* 2.7 57.7 + - + +
208B VAL* 3.8 16.8 - - + -
212B TRP* 4.2 15.3 - - - -
213B PHE* 3.7 22.9 - - + -
260B MET* 3.7 16.6 - - + -
264B LEU* 3.7 37.0 - - + -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LYS 5.1 0.2 - - - +
125B ILE* 3.4 7.6 - - - +
126B THR* 2.7 57.7 + - - +
128B ASN* 5.2 6.5 - - - +
198B LEU 3.9 2.6 + - - +
199B MET* 1.3 71.3 - - - +
201B MET* 1.3 63.0 + - - +
202B LYS 4.1 16.9 + - - +
203B LYS* 4.9 6.3 - - - +
204B LYS 3.6 6.7 - - - +
205B THR* 3.4 27.1 - - + +
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Residues in contact with MET 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.0 18.2 - - + -
124B LYS 5.7 1.6 - - - +
125B ILE* 3.8 30.5 - - + +
199B MET* 4.3 1.0 + - + -
200B LYS* 1.3 73.7 - - - +
202B LYS* 1.4 61.9 + - + +
203B LYS 2.8 16.8 + - - -
204B LYS* 2.8 24.3 + - - +
206B TRP* 3.7 21.9 - - + -
257B GLU* 3.7 41.3 - - + +
260B MET* 3.9 23.8 - - + -
261B HIS* 4.5 13.5 - - - -
264B LEU* 4.8 3.1 - - - -
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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