Contacts of the helix formed by residues 195 - 208 (chain A) in PDB entry 1U5T
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 ALA 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ILE* 3.0 30.3 - - + +
188A LYS* 4.0 22.9 - - + +
194A GLU* 1.3 93.6 + - - +
196A VAL* 1.3 62.5 + - - +
198A SER* 3.5 8.6 - - - -
199A LYS* 3.7 4.9 + - - +
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Residues in contact with VAL 196 (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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194A GLU* 3.6 7.5 + - - +
195A ALA* 1.3 74.3 - - - +
197A ARG* 1.3 63.4 - - + +
198A SER 2.1 20.1 + - - -
199A LYS* 3.1 3.1 + - - +
200A SER* 2.7 28.6 + - - +
87D GLN* 4.5 27.6 - - + -
88D VAL* 3.9 22.9 - - + +
91D ASP* 5.9 1.3 - - - +
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Residues in contact with ARG 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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168A ASP* 4.6 4.0 + - - -
193A TRP* 3.4 63.2 - - + -
194A GLU* 4.2 15.2 - - + +
195A ALA 4.9 0.7 - - - -
196A VAL* 1.3 83.6 - - + +
198A SER* 1.3 58.2 + - - +
200A SER* 3.2 12.3 - - - -
201A ALA* 4.1 6.7 - - - +
88D VAL* 4.7 16.4 - - + -
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ILE* 3.7 11.6 + - - +
187A LEU* 3.2 39.8 - - - +
193A TRP* 4.6 1.6 - - - +
194A GLU 3.9 6.3 + - - -
195A ALA* 3.5 22.9 - - - -
196A VAL 2.1 19.8 + - - -
197A ARG 1.3 69.9 + - - -
199A LYS* 1.3 55.1 + - - -
200A SER* 3.1 0.4 + - - -
201A ALA* 2.9 4.3 + - - +
202A LEU* 2.5 42.3 + - - +
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Residues in contact with LYS 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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184A ILE* 4.0 22.7 - - + +
195A ALA 3.7 7.1 + - - +
196A VAL* 3.1 5.4 + - - +
198A SER* 1.3 72.4 - - - +
200A SER* 1.3 57.9 + - - +
202A LEU* 2.5 32.9 + - - -
203A ASP* 2.8 44.2 + - - +
213A ILE* 6.1 0.2 - - - +
215A TYR* 5.7 2.6 + - - -
221A ALA* 5.5 6.7 - - - +
223A TYR* 3.5 18.9 + - + +
551B LEU* 5.5 6.3 - - - +
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Residues in contact with SER 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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196A VAL* 2.7 24.1 + - - -
197A ARG* 3.2 13.5 - - - -
199A LYS* 1.3 81.5 - - - +
201A ALA* 1.3 71.6 + - - +
203A ASP* 3.5 10.9 + - - +
204A GLU* 3.5 14.6 + - - +
86D SER* 5.1 5.8 - - - -
88D VAL* 4.2 20.1 - - - +
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Residues in contact with ALA 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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168A ASP* 4.9 21.1 - - + +
169A GLN* 4.4 6.6 + - - +
172A ILE* 5.3 5.8 - - + +
187A LEU* 6.2 0.7 - - + -
193A TRP* 5.3 1.8 - - + +
197A ARG* 4.1 13.5 - - - +
198A SER* 2.9 9.2 + - - +
200A SER* 1.3 84.0 + - - +
202A LEU* 1.3 64.6 + - + +
204A GLU* 3.9 6.3 + - - +
205A MET* 3.6 20.6 + - - +
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Residues in contact with LEU 202 (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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172A ILE* 3.3 42.2 - - + -
182A SER* 4.0 2.5 - - - +
183A SER* 4.1 26.0 - - - +
184A ILE* 4.4 4.5 - - + +
187A LEU* 3.9 15.9 - - + -
198A SER* 2.5 18.3 + - - +
199A LYS* 2.5 12.0 + - - +
201A ALA* 1.3 72.0 - - + +
203A ASP* 1.3 61.8 + - - +
205A MET* 3.1 19.3 - - - +
206A VAL* 3.5 2.4 - - - +
211A LEU* 5.1 0.4 - - + -
223A TYR* 3.2 59.1 - - + -
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Residues in contact with ASP 203 (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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199A LYS* 2.8 48.2 + - - +
200A SER* 4.1 5.7 + - - +
202A LEU* 1.3 69.6 - - - +
204A GLU* 1.3 58.5 + - - +
205A MET 2.8 1.1 - - - -
206A VAL* 2.4 33.8 + - + +
207A ALA* 2.8 11.9 + - - +
213A ILE* 4.8 0.7 - - - +
223A TYR* 2.4 32.1 + - - -
551B LEU* 4.2 16.6 - - + +
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Residues in contact with GLU 204 (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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169A GLN* 3.8 18.7 + - - +
200A SER 3.5 11.1 + - - +
201A ALA* 4.1 9.0 - - - +
202A LEU 3.4 0.2 - - - -
203A ASP* 1.3 76.5 - - - +
205A MET* 1.3 65.3 + - - +
206A VAL 2.7 2.1 + - - -
207A ALA* 2.9 6.2 + - + +
208A ASN* 2.8 41.2 + - - +
549B LYS* 3.0 30.6 + - + +
16D ARG* 3.0 33.3 + - - +
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Residues in contact with MET 205 (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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169A GLN* 3.0 52.7 - - + +
172A ILE* 3.7 29.4 - - - -
173A LEU* 4.2 21.3 - - + +
201A ALA 3.6 6.9 + - - +
202A LEU* 3.1 14.5 + - - +
203A ASP 2.8 0.6 - - - -
204A GLU* 1.3 80.9 - - - +
206A VAL* 1.3 55.0 + - - +
208A ASN* 4.1 4.7 - - - -
209A GLY 3.7 0.5 + - - -
210A LEU* 3.1 41.2 + - + +
211A LEU* 2.9 46.2 + - + +
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Residues in contact with VAL 206 (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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202A LEU 3.5 13.9 - - - +
203A ASP* 2.4 34.4 + - - +
204A GLU 2.7 0.2 + - - -
205A MET* 1.3 69.7 - - + +
207A ALA* 1.3 61.2 + - - +
208A ASN 3.1 1.3 - - - -
209A GLY* 2.7 18.0 + - - +
211A LEU* 3.5 20.4 - - + +
213A ILE* 4.0 21.3 - - + +
223A TYR* 4.0 16.8 - - + -
551B LEU* 3.3 21.3 - - + -
17C GLN* 4.4 5.4 - - - +
18C PRO* 4.2 14.6 - - + -
19C ASN* 3.0 16.3 - - + +
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Residues in contact with ALA 207 (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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203A ASP 2.8 10.0 + - - +
204A GLU* 3.8 8.5 - - - +
206A VAL* 1.3 76.0 - - - +
208A ASN* 1.3 60.6 + - - +
209A GLY 3.1 3.6 + - - -
549B LYS* 4.0 23.3 - - + -
550B GLN 3.1 27.1 - - - +
551B LEU* 3.7 14.4 - - - +
553B GLY* 4.1 6.9 - - - +
554B ILE* 3.7 13.7 - - - +
19C ASN* 3.2 10.2 - - - +
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Residues in contact with ASN 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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111A GLY* 4.5 9.2 - - - +
163A ASN* 4.9 14.3 - - - +
169A GLN* 5.1 8.6 + - - +
204A GLU* 2.8 32.4 + - - +
205A MET* 4.6 4.3 - - - +
207A ALA* 1.3 78.4 - - - +
209A GLY* 1.3 61.4 + - - +
210A LEU* 3.4 16.4 + - + +
549B LYS* 3.7 34.2 + - - +
554B ILE* 4.1 8.6 - - - +
19C ASN* 4.2 0.2 - - - -
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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