Contacts of the strand formed by residues 211 - 217 (chain A) in PDB entry 1UKW
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 VAL 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LEU* 6.0 0.2 - - + -
165A ALA* 5.1 5.2 - - - +
167A LEU* 4.5 17.5 - - + +
199A PHE* 4.3 15.3 - - + -
200A ALA 3.2 12.3 - - - +
201A THR* 5.0 3.8 - - - -
207A ARG 4.0 11.0 - - - +
208A HIS* 3.1 21.3 + - - +
210A GLY* 1.3 78.2 - - - +
212A VAL* 1.3 67.7 - - - +
259A GLY* 3.1 16.3 + - - -
261A GLY* 2.9 24.3 + - - -
262A PHE* 3.5 33.7 - - + +
265A ALA* 6.0 0.2 - - + -
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Residues in contact with VAL 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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171A ALA* 4.1 23.6 - - + -
178A TYR* 4.5 6.1 - - + +
198A VAL 3.8 0.7 - - - +
199A PHE* 3.6 2.4 - - - -
200A ALA 2.8 34.7 + - - +
202A VAL* 5.0 7.9 - - + -
210A GLY 4.9 3.8 - - - +
211A VAL* 1.3 75.3 - - - +
213A ALA* 1.3 63.4 + - - +
214A LEU* 4.0 14.8 - - + +
254A ARG* 3.4 36.8 - - + -
255A LEU 5.4 0.2 - - - +
257A GLU 4.3 2.0 - - - +
258A GLU* 4.0 21.5 - - + -
259A GLY 4.7 0.2 - - - +
261A GLY* 3.8 9.2 - - - +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A VAL* 4.4 7.2 - - + -
198A VAL 3.6 4.0 - - - -
199A PHE* 3.8 28.3 - - + -
212A VAL* 1.3 76.7 - - - +
214A LEU* 1.3 67.4 + - - +
254A ARG* 3.4 1.9 - - - +
255A LEU* 2.9 49.8 + - + +
257A GLU 5.5 0.2 + - - -
261A GLY* 3.9 3.5 - - - +
264A ILE* 4.2 10.8 - - + -
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Residues in contact with LEU 214 (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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171A ALA* 4.1 26.0 - - + -
178A TYR* 4.0 28.3 - - + -
180A LEU* 4.5 13.0 - - + -
196A VAL 3.4 0.7 - - - +
197A VAL* 4.4 2.2 - - - +
198A VAL* 2.7 47.6 + - + +
200A ALA* 5.3 2.0 - - + -
212A VAL* 4.0 14.1 - - + -
213A ALA* 1.3 85.1 - - - +
215A VAL* 1.3 61.9 + - - +
216A VAL* 3.6 5.2 + - + +
249A VAL* 4.0 22.2 - - + -
253A ASN 3.5 2.2 - - - -
254A ARG* 3.6 29.6 - - + +
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Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL* 4.4 6.7 - - + -
140A PHE* 3.5 39.0 - - + -
195A TRP* 3.5 35.9 - - + -
196A VAL 3.6 3.4 - - - +
197A VAL* 4.3 5.6 - - + +
214A LEU* 1.3 73.7 - - - +
216A VAL* 1.3 62.1 + - - +
249A VAL* 3.6 8.8 - - - +
253A ASN* 2.9 32.8 + - - +
255A LEU* 3.6 38.6 - - + -
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Residues in contact with VAL 216 (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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180A LEU* 3.9 27.1 - - + -
195A TRP* 3.0 4.1 - - - -
196A VAL* 2.7 42.9 + - + +
198A VAL* 4.1 16.2 - - + -
214A LEU* 4.1 4.7 - - + +
215A VAL* 1.3 78.3 - - - +
217A GLU* 1.3 65.6 + - - +
218A ARG 3.8 0.2 + - - -
220A THR* 4.1 10.8 - - + +
223A PHE* 3.7 30.0 - - + -
244A PHE* 4.1 8.7 - - + -
247A VAL* 4.6 6.3 - - + -
249A VAL* 4.0 13.2 - - + -
253A ASN* 5.1 0.2 - - - +
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Residues in contact with GLU 217 (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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139A ARG* 4.6 5.7 + - - -
140A PHE* 4.0 12.5 - - + -
194A GLU 3.6 7.0 - - - +
195A TRP* 4.1 11.0 - - + +
216A VAL* 1.3 76.2 - - - +
218A ARG* 1.3 55.0 + - - +
219A GLY 2.7 17.0 + - - +
220A THR* 2.6 34.1 + - - +
223A PHE* 3.7 6.1 - - - -
253A ASN* 3.3 27.2 + - - +
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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