Contacts of the helix formed by residues 207 - 215 (chain A) in PDB entry 1UK0
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 ASN 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 3.4 22.5 + - - +
109A ASP* 3.0 35.6 - - - +
203A SER* 2.6 30.1 + - - +
204A ARG* 3.3 27.3 - - - +
205A THR 4.1 0.7 - - - +
206A THR* 1.3 76.8 + - - +
208A PHE* 1.3 52.0 + - - +
209A ALA 3.5 0.7 - - - -
210A GLY 2.9 8.5 + - - -
211A ILE* 2.8 34.6 + - + +
501A FRM 3.3 19.2 - - - -
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Residues in contact with PHE 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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15A ILE* 4.4 4.0 - - + -
201A HIS 4.5 0.2 - - - -
203A SER* 3.3 44.0 - - - -
205A THR* 3.3 25.9 + - - +
207A ASN* 1.3 71.8 - - - +
209A ALA* 1.3 71.8 + - - +
210A GLY 3.2 0.9 - - - -
211A ILE* 3.7 13.9 - - + -
212A LEU* 2.8 39.9 + - + +
257A LEU* 3.5 36.8 - - + -
258A ILE* 4.1 4.3 - - - -
259A LEU* 3.4 42.0 - - + -
341A LEU* 3.9 22.2 - - + -
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Residues in contact with ALA 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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15A ILE* 3.2 29.8 + - - +
16A PHE* 4.6 10.5 - - + -
113A ALA* 3.5 33.7 - - + -
116A LEU* 5.0 5.4 - - - +
136A LEU* 4.1 17.7 - - - +
205A THR 4.0 3.2 + - - -
206A THR 4.2 4.2 + - - +
208A PHE* 1.3 78.9 - - - +
210A GLY* 1.4 57.6 + - - +
213A SER* 3.0 19.2 + - - -
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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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109A ASP* 4.0 10.1 + - - -
112A VAL* 4.5 16.2 - - - -
113A ALA 4.7 0.4 - - - +
207A ASN 2.9 13.3 + - - -
209A ALA* 1.4 74.5 - - - +
211A ILE* 1.3 55.5 + - - -
212A LEU 3.1 0.9 - - - -
213A SER* 3.0 10.5 - - - -
214A GLN* 2.4 38.3 + - - +
217A ARG* 3.3 8.1 + - - -
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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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109A ASP* 3.3 13.0 - - - +
180A ARG* 3.9 4.5 - - - -
203A SER* 3.9 20.2 - - - +
207A ASN* 2.8 17.6 + - + +
208A PHE* 3.7 35.4 - - + +
210A GLY* 1.3 73.5 - - - -
212A LEU* 1.3 62.1 + - + +
215A GLY* 3.2 16.9 + - - -
216A LEU* 3.6 30.5 - - + +
217A ARG* 3.7 6.7 - - - +
259A LEU* 3.5 26.2 - - + -
338A LEU* 3.9 11.5 - - + +
501A FRM 6.0 0.2 - - + -
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Residues in contact with LEU 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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15A ILE* 3.9 19.3 - - + -
136A LEU* 3.1 19.7 - - + +
138A THR* 3.2 36.9 + - + +
140A ILE* 3.9 15.5 - - + -
178A ILE* 3.7 23.6 - - + -
180A ARG* 2.9 28.5 + - - +
208A PHE* 2.8 48.4 + - + +
210A GLY 3.1 0.2 - - - -
211A ILE* 1.3 83.4 - - + +
213A SER* 1.3 61.6 + - - +
259A LEU* 6.0 0.7 - - + -
338A LEU* 5.5 2.0 - - + -
341A LEU* 4.4 11.7 - - + -
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Residues in contact with SER 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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112A VAL* 4.4 3.5 - - - +
116A LEU* 3.7 24.9 - - - +
135A LYS 4.2 7.6 - - - -
136A LEU* 3.1 17.0 + - - +
137A LYS* 6.0 0.2 - - - -
180A ARG* 3.2 13.7 + - - +
209A ALA 3.0 19.2 + - - -
210A GLY* 3.0 8.7 - - - -
212A LEU* 1.3 80.3 - - - +
214A GLN* 1.3 82.1 + - - -
215A GLY 3.3 0.4 - - - -
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Residues in contact with GLN 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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112A VAL* 4.4 22.1 - - + +
116A LEU* 6.0 0.8 - - - +
180A ARG* 3.4 6.4 + - - -
186A ARG* 5.4 2.1 + - - -
210A GLY 2.4 23.3 + - - +
213A SER* 1.3 90.3 + - - +
215A GLY* 1.4 64.9 + - - +
216A LEU 4.3 1.4 - - - +
217A ARG* 3.0 38.6 + - - +
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Residues in contact with GLY 215 (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 ARG* 3.0 35.8 - - - +
183A GLU* 4.4 4.0 - - - -
186A ARG* 5.2 4.3 - - - -
211A ILE* 3.2 14.4 + - - -
214A GLN* 1.4 87.9 - - - +
216A LEU* 1.3 65.1 + - - -
217A ARG* 2.8 22.2 + - - -
338A LEU* 5.0 0.7 - - - -
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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