Contacts of the strand formed by residues 214 - 224 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B THR 3.9 2.0 - - - -
150B LEU* 4.0 15.5 - - + -
156B PHE* 4.0 15.3 - - + -
174B ILE* 4.2 2.0 - - + -
192B LEU 3.5 2.1 - - - +
193B VAL* 3.4 2.6 - - - -
194B ILE* 2.8 40.6 + - + +
199B ALA* 3.8 25.8 - - + -
200B TYR* 3.9 23.1 - - + -
208B ILE* 3.8 24.7 - - + -
212B SER* 3.8 9.6 - - - +
213B THR* 1.3 81.7 - - - +
215B VAL* 1.3 61.3 + - - +
216B PHE* 3.7 30.3 - - + -
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B TYR* 3.8 34.5 - - + +
147B LYS 3.6 1.0 - - - +
148B GLY* 3.4 1.9 - - - -
149B THR* 2.8 55.2 + - - +
150B LEU 4.4 5.8 - - - +
151B ILE* 4.3 11.4 - - + -
191B LYS* 4.0 28.7 - - + -
192B LEU 3.3 6.5 - - - +
193B VAL* 4.4 6.3 - - + -
214B LEU* 1.3 76.0 - - - +
216B PHE* 1.3 64.4 + - - +
217B ASP* 4.9 8.0 - - - +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 4.0 13.9 - + - -
147B LYS 3.1 6.5 - - - +
148B GLY* 3.7 20.9 - - - -
156B PHE* 3.6 22.9 - + - -
157B ASP* 5.6 0.4 - - - -
174B ILE* 4.3 4.9 - - + -
177B TRP* 3.3 44.4 - + - +
190B ILE 3.8 0.9 - - - +
191B LYS* 3.3 6.9 - - - +
192B LEU* 2.8 41.9 + - + +
194B ILE* 3.8 19.7 - - + -
200B TYR* 5.8 2.0 - + - -
214B LEU* 3.7 30.7 - - + -
215B VAL* 1.3 76.7 - - - +
217B ASP* 1.3 63.9 + - - +
218B VAL* 3.8 15.2 - - + +
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Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B TYR* 3.1 5.5 - - - -
147B LYS* 2.8 56.3 + - + +
149B THR* 5.7 1.2 + - - +
160B TYR* 5.4 1.7 + - - -
190B ILE 4.0 2.0 - - - -
191B LYS* 3.7 29.7 - - - +
215B VAL* 4.9 8.0 - - - +
216B PHE* 1.3 72.8 - - - +
218B VAL* 1.3 60.8 + - - +
219B GLU* 5.6 1.9 - - - +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 4.0 21.8 - - + -
145B ASN 3.6 9.2 - - - +
146B TYR* 4.2 8.5 - - + -
177B TRP* 4.2 12.1 - - + -
181B LEU* 3.9 18.2 - - + -
184B ILE* 5.8 0.4 - - + -
189B LYS* 3.2 7.3 - - - +
190B ILE* 2.9 44.5 + - + +
192B LEU* 4.3 15.0 - - + -
216B PHE* 3.9 21.3 - - + -
217B ASP* 1.3 79.5 - - - +
219B GLU* 1.3 68.6 + - - +
220B LEU* 4.2 1.6 - - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 3.2 7.8 - - - +
145B ASN* 2.9 53.2 + - + +
160B TYR* 3.3 22.0 + - - +
188B GLY 3.6 4.9 - - - +
189B LYS* 3.8 34.9 - - + +
217B ASP 5.6 1.1 - - - +
218B VAL* 1.3 77.7 - - - +
220B LEU* 1.3 60.9 + - - +
221B LEU* 3.5 11.1 + - + +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PRO* 4.3 5.8 - - + -
142B VAL* 3.8 22.4 - - + -
143B VAL 3.9 4.9 - - - +
144B VAL* 3.9 9.0 - - + -
181B LEU* 4.5 10.1 - - + +
184B ILE* 3.8 30.5 - - + +
185B LYS* 3.4 33.0 - - - +
186B LYS* 3.8 2.7 - - - +
187B GLY* 2.8 32.6 + - - -
188B GLY 2.9 10.3 + - - +
218B VAL* 4.2 2.8 + - + -
219B GLU* 1.3 69.0 - - - +
221B LEU* 1.3 59.6 + - - +
222B ASP 3.5 22.0 - - - +
223B VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 2.8 23.1 + - + +
144B VAL* 4.2 0.7 - - - -
145B ASN* 3.6 30.7 - - - +
165B PRO* 3.7 33.4 - - + -
186B LYS* 3.6 20.5 - - - +
187B GLY* 4.6 2.9 + - - +
219B GLU* 4.0 18.8 - - + +
220B LEU* 1.3 78.0 - - - +
222B ASP* 1.3 60.2 + - + +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B THR 4.4 0.4 - - - -
142B VAL* 3.4 4.6 - - - -
143B VAL* 3.0 43.1 + - + +
186B LYS* 3.1 31.0 + - - +
220B LEU* 3.5 4.8 - - - +
221B LEU* 1.3 79.2 - - + +
223B VAL* 1.3 79.4 + - - +
224B LYS* 3.6 24.7 + - - +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU* 4.6 18.4 - - + +
136B PRO* 4.4 15.0 - - + -
140B ASP* 3.6 29.4 - - + +
141B THR 3.5 4.7 - - - -
142B VAL* 4.2 5.4 - - + -
186B LYS* 4.2 19.9 - - + +
220B LEU* 3.8 28.5 - - + -
222B ASP* 1.3 86.7 + - - +
224B LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B SER 5.0 0.2 - - - +
140B ASP* 3.5 14.8 - - - +
141B THR* 2.8 61.8 + - - +
143B VAL* 4.2 18.7 - - + +
167B SER* 4.6 3.4 + - - -
222B ASP* 3.6 25.8 + - - +
223B VAL* 1.3 76.9 - - - +
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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