Contacts of the strand formed by residues 214 - 224 (chain A) in PDB entry 1Q6H
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 LEU 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A THR 4.0 1.8 - - - -
150A LEU* 4.3 2.9 - - + -
156A PHE* 3.9 20.0 - - + -
174A ILE* 4.1 2.9 - - + -
192A LEU 3.4 4.0 - - - +
193A VAL* 3.4 1.4 - - - -
194A ILE* 2.8 41.6 + - + +
199A ALA* 3.6 26.7 - - + -
200A TYR* 3.8 21.8 - - + -
208A ILE* 3.8 25.8 - - + -
212A SER* 3.8 13.0 - - - +
213A THR* 1.3 81.3 - - - +
215A VAL* 1.3 61.9 + - - +
216A PHE* 3.7 32.3 - - + -
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Residues in contact with VAL 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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106A TYR* 3.8 33.2 - - + +
147A LYS 3.6 1.4 - - - +
148A GLY* 3.3 2.6 - - - -
149A THR* 2.7 61.2 + - - +
151A ILE* 4.2 16.6 - - + -
191A LYS* 3.9 30.7 - - + +
192A LEU 3.4 7.0 - - - +
193A VAL* 4.3 5.4 - - + -
214A LEU* 1.3 75.9 - - - +
216A PHE* 1.3 63.2 + - - +
217A ASP* 5.3 5.2 - - - +
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Residues in contact with PHE 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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146A TYR* 3.9 19.5 - + - -
147A LYS 3.2 3.4 - - - -
148A GLY* 3.8 13.9 - - - -
156A PHE* 3.5 29.6 - + - -
157A ASP* 5.4 0.9 - - - -
174A ILE* 4.4 3.1 - - + -
177A TRP* 3.4 40.8 - + + -
190A ILE 3.7 1.0 - - - +
191A LYS* 3.3 5.9 - - - +
192A LEU* 2.8 45.0 + - + +
194A ILE* 3.6 20.0 - - + -
200A TYR* 5.8 2.5 - + - -
214A LEU* 3.7 31.4 - - + -
215A VAL* 1.3 73.2 - - - +
217A ASP* 1.3 62.2 + - - +
218A VAL* 3.7 15.3 + - + +
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Residues in contact with ASP 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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146A TYR* 3.1 4.7 - - - -
147A LYS* 2.9 56.7 + - + +
160A TYR* 5.0 3.9 + - + -
190A ILE 4.0 3.1 - - - -
191A LYS* 3.7 28.7 - - - +
215A VAL* 4.3 5.2 - - - +
216A PHE* 1.3 71.0 - - - +
218A VAL* 1.3 59.9 + - - +
219A GLU* 6.0 0.2 - - - -
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Residues in contact with VAL 218 (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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144A VAL* 3.9 10.1 - - + -
145A ASN 3.5 7.2 - - - +
146A TYR* 4.2 0.4 - - + -
177A TRP* 3.5 42.6 - - + -
181A LEU* 3.8 14.6 - - + -
189A LYS* 3.1 7.3 - - - +
190A ILE* 2.9 47.3 + - + +
192A LEU* 4.3 11.9 - - + -
216A PHE* 3.7 20.0 - - + +
217A ASP* 1.3 78.8 - - - +
219A GLU* 1.3 67.7 + - - +
220A LEU 4.1 0.7 - - - +
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Residues in contact with GLU 219 (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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144A VAL* 3.2 6.4 - - - -
145A ASN* 2.7 50.7 + - + +
160A TYR* 3.3 26.2 + - - +
188A GLY 3.6 5.2 - - - +
189A LYS* 3.5 38.3 - - + +
217A ASP 6.0 0.2 - - - -
218A VAL* 1.3 79.6 - - - +
220A LEU* 1.3 60.7 + - - +
221A LEU* 3.5 14.2 + - + +
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Residues in contact with LEU 220 (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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136A PRO* 3.9 24.2 - - + -
142A VAL* 4.1 13.2 - - + -
143A VAL 3.7 7.2 - - - +
144A VAL* 3.9 15.3 - - + -
181A LEU* 4.5 8.3 - - + +
184A ILE* 3.7 27.5 - - + +
185A LYS* 3.4 31.2 - - - +
186A LYS* 3.9 4.5 - - - +
187A GLY* 2.7 35.9 + - - -
188A GLY 2.9 9.1 + - - +
218A VAL* 4.1 1.2 - - - +
219A GLU* 1.3 69.6 - - - +
221A LEU* 1.3 57.5 + - - +
222A ASP 3.5 22.7 - - - +
223A VAL* 4.0 4.0 - - + -
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Residues in contact with LEU 221 (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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143A VAL* 2.7 22.8 + - + +
145A ASN* 3.5 31.0 - - - +
165A PRO* 3.7 28.9 - - + -
186A LYS* 3.5 21.1 - - - +
187A GLY* 4.5 2.7 + - - +
219A GLU* 4.0 21.3 - - + +
220A LEU* 1.3 77.4 - - - +
222A ASP* 1.3 60.2 + - + +
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Residues in contact with ASP 222 (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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141A THR 4.6 0.2 - - - -
142A VAL* 3.5 4.3 - - - -
143A VAL* 3.1 41.8 + - + -
186A LYS* 3.0 32.8 + - - +
220A LEU* 3.5 4.6 - - - +
221A LEU* 1.3 81.6 - - + +
223A VAL* 1.3 85.2 + - - +
224A LYS* 3.4 26.9 + - + +
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Residues in contact with VAL 223 (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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134A GLU* 4.5 13.7 - - + +
135A ALA 4.9 1.1 - - - -
136A PRO* 4.0 26.7 - - + -
140A ASP* 3.7 28.7 - - + +
141A THR 3.5 4.0 - - - +
142A VAL* 4.7 2.5 - - + +
186A LYS* 4.3 19.2 - - + +
220A LEU* 4.0 26.5 - - + -
222A ASP* 1.3 87.9 + - - +
224A LYS* 1.3 64.6 + - - +
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Residues in contact with LYS 224 (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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140A ASP* 3.6 14.1 - - - +
141A THR* 2.7 63.0 + - - +
143A VAL* 3.6 28.4 - - + +
167A SER* 5.0 3.3 + - - -
222A ASP* 3.4 21.9 + - - +
223A VAL* 1.3 76.2 - - - +
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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