Contacts of the strand formed by residues 196 - 201 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.4 1.4 - - - +
130A VAL* 4.0 17.4 + - + +
191A ILE* 3.8 34.8 - - + -
192A ASP 3.3 18.2 - - - +
193A PHE* 3.2 22.1 + - + +
194A ASN 3.5 1.2 - - - +
195A GLU* 1.4 83.4 - - + +
197A ILE* 1.3 73.0 + - - +
207A LEU* 4.4 24.5 - - + +
208A VAL* 3.4 26.9 - - - +
209A HIS* 3.5 36.6 - - + +
210A LYS* 4.4 1.8 - - - +
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.8 20.4 - - + -
127A GLY* 4.1 15.3 - - - -
128A ASN 3.9 5.6 - - - +
129A LEU* 3.8 40.2 - - + +
130A VAL* 4.5 3.1 - - - -
196A MET* 1.3 81.4 - - - +
198A LEU* 1.3 61.9 - - - +
199A MET 3.2 6.1 + - - +
206A TRP 3.7 0.2 - - - +
207A LEU* 3.9 1.7 - - - -
208A VAL* 2.7 39.8 + - + +
209A HIS 4.3 6.1 - - - +
210A LYS* 3.8 27.6 - - + +
213A PHE* 4.0 29.6 - - + -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 4.5 19.1 - - + +
53A VAL* 4.5 16.6 - - + -
127A GLY* 3.7 0.5 - - - -
128A ASN* 2.8 45.0 + - + +
130A VAL* 4.1 15.2 - - + +
197A ILE* 1.3 67.6 - - - +
199A MET* 1.3 61.1 + - - +
200A LYS* 3.9 2.6 + - - +
205A THR* 3.9 22.7 + - + +
206A TRP 3.6 3.6 - - - +
207A LEU* 3.9 14.4 - - + +
270A VAL* 3.9 17.9 - - + -
279A PHE* 3.7 28.0 - - + -
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 3.8 19.5 - - + -
126A THR 3.5 12.3 - - - +
127A GLY* 4.1 2.2 - - - -
197A ILE* 3.2 2.1 + - + -
198A LEU* 1.3 73.0 - - - +
200A LYS* 1.3 55.7 + - - +
201A MET* 4.3 10.3 - - + -
205A THR* 2.8 6.8 + - - -
206A TRP* 2.7 55.7 + - + +
208A VAL* 3.8 18.2 - - + -
212A TRP* 4.2 16.4 - - - -
213A PHE* 3.7 22.0 - - + -
260A MET* 3.7 26.2 - - + -
264A LEU* 4.0 30.1 - - + -
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS 5.1 0.3 - - - +
125A ILE* 3.4 21.4 - - - +
126A THR* 2.8 39.9 + - + +
128A ASN* 5.4 2.0 - - - +
198A LEU* 3.9 3.5 + - - +
199A MET* 1.3 73.3 - - - +
201A MET* 1.3 65.2 + - - +
202A LYS 4.2 12.0 + - - +
203A LYS 4.8 8.3 - - - +
204A LYS 3.5 12.6 - - - +
205A THR* 3.7 23.6 - - - +
271A ASP* 5.7 1.8 - - - -
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Residues in contact with MET 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.5 4.0 - - + -
125A ILE* 3.7 29.6 - - + -
199A MET* 4.3 8.0 + - + -
200A LYS* 1.3 71.9 - - - +
202A LYS* 1.4 66.6 + - + +
203A LYS 2.9 16.1 + - - -
204A LYS* 2.7 24.2 + - - +
206A TRP* 3.6 21.5 - - + -
257A GLU* 3.8 28.9 - - + -
260A MET* 3.7 36.1 - - + -
261A HIS* 3.9 28.0 - - - +
264A LEU* 4.6 2.5 - - - -
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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