Contacts of the strand formed by residues 207 - 213 (chain A) in PDB entry 3UNF
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 ILE 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA* 6.1 0.4 - - + -
47A THR 3.4 10.5 - - - +
48A GLU* 4.6 1.1 - - - -
49A LYS* 4.0 4.9 - - - +
191A ILE* 5.2 6.5 - - + -
194A LEU* 3.5 27.1 - - + -
198A PHE* 4.0 11.7 - - + -
202A MET* 4.0 23.8 - - + -
203A THR 3.3 23.6 - - - +
204A GLU* 3.3 17.5 - - - +
205A ASP 4.4 1.4 - - - +
206A ASN* 1.3 83.1 - - + +
208A GLU* 1.3 64.0 + - - +
209A VAL* 5.0 3.8 - - + -
225A VAL* 3.7 31.6 - - + +
229A LEU* 4.1 18.8 - - + -
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Residues in contact with GLU 208 (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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46A ALA* 3.3 3.2 - - - +
47A THR* 2.8 46.9 + - + +
49A LYS* 3.1 35.4 + - + +
62A HIS* 3.3 8.8 - - - +
63A LYS* 3.0 23.4 + - - +
64A VAL* 2.8 29.2 + - + +
207A ILE* 1.3 75.4 - - - +
209A VAL* 1.3 63.9 + - - +
219A ARG* 3.1 33.2 + - + -
225A VAL* 5.9 0.7 - - - -
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Residues in contact with VAL 209 (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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44A VAL* 3.8 24.0 - - + -
45A LEU 3.2 10.1 - - - +
46A ALA* 4.0 11.0 - - + -
64A VAL* 4.4 3.8 - - - -
187A ILE* 4.2 6.7 - - + -
190A ALA* 6.1 0.2 - - + -
191A ILE* 5.0 9.0 - - + -
207A ILE* 5.0 4.9 - - + -
208A GLU* 1.3 81.0 - - - +
210A GLY* 1.3 62.8 + - - +
211A ILE* 4.7 0.2 - - + -
219A ARG* 3.8 4.8 - - - +
220A LEU* 2.9 48.4 + - + +
225A VAL* 3.9 35.4 - - + +
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Residues in contact with GLY 210 (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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44A VAL* 3.5 1.7 - - - +
45A LEU* 2.8 35.4 + - - +
64A VAL* 3.8 20.8 - - - +
209A VAL* 1.3 72.7 - - - +
211A ILE* 1.3 68.0 + - - +
217A PHE* 4.1 7.6 - - - -
218A ARG 3.4 10.1 - - - -
219A ARG* 3.9 3.1 - - - -
220A LEU 4.3 0.2 - - - -
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Residues in contact with ILE 211 (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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43A VAL 3.4 7.2 - - - +
44A VAL* 4.1 7.9 - - + -
136A CYS* 5.3 0.2 - - - -
183A LEU* 4.3 20.0 - - + -
187A ILE* 3.9 33.7 - - + -
210A GLY* 1.3 77.5 - - - +
212A CYS* 1.3 61.6 + - - +
213A ASN* 4.4 11.0 - - - +
216A GLY 4.0 0.7 - - - +
217A PHE* 3.2 7.1 - - - -
218A ARG* 2.8 68.1 + - + +
220A LEU* 4.0 27.4 - - + -
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Residues in contact with CYS 212 (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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42A GLY* 3.2 5.9 - - - -
43A VAL* 2.8 44.5 + - + +
70A HIS 3.3 28.3 - - - -
136A CYS* 3.7 22.0 - - - -
137A GLY* 3.7 9.9 - - - -
138A TRP* 3.6 24.1 - - - -
183A LEU* 4.2 2.3 - - - +
211A ILE* 1.3 76.2 - - - +
213A ASN* 1.3 64.6 + - - +
216A GLY 3.4 9.9 - - - -
217A PHE* 3.9 4.9 - - + -
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Residues in contact with ASN 213 (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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41A ASN 4.1 13.5 - - - +
138A TRP* 3.3 31.6 - - - +
183A LEU* 4.2 17.6 - - + +
211A ILE* 4.9 10.6 - - - +
212A CYS* 1.3 74.8 - - - +
214A GLU* 1.3 68.1 + - + +
215A ALA* 3.1 22.4 + - - +
216A GLY* 2.9 27.1 + - - +
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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