Contacts of the strand formed by residues 204 - 211 (chain B) in PDB entry 1ZQ9
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 SER 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B MET* 3.9 20.2 - - - -
155B PHE 3.3 13.7 + - - -
156B GLN* 4.5 4.0 - - - +
157B ARG* 2.8 14.6 + - - +
191B VAL* 2.6 45.4 + - - -
193B LYS* 5.8 0.2 - - - -
196B PHE* 3.9 17.8 - - - -
200B PRO* 4.3 5.5 - - - +
202B VAL* 4.1 7.1 + - - +
203B GLU* 1.3 77.3 + - - +
205B SER* 1.3 57.8 + - - +
4001B SAM 4.6 5.9 + - - -
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU 3.6 0.7 - - - +
154B MET* 3.4 5.5 - - - +
155B PHE* 2.8 33.1 + - - +
157B ARG* 2.8 28.7 + - - +
160B ALA* 3.5 22.1 - - - +
187B HIS* 2.7 34.1 + - - -
189B MET 3.2 6.0 + - - -
191B VAL 4.3 1.1 - - - +
204B SER* 1.3 70.2 + - - +
206B VAL* 1.3 64.7 + - - +
207B VAL* 3.9 0.9 + - - +
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Residues in contact with VAL 206 (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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48B ILE* 4.0 22.0 - - + -
152B ILE* 3.4 32.1 - - + -
153B LEU 3.4 7.6 - - - +
154B MET* 3.8 21.8 - - + -
187B HIS* 3.8 1.7 + - - -
188B LEU* 2.7 43.0 + - + +
189B MET* 2.8 44.3 + - + +
191B VAL* 3.8 7.0 - - + -
205B SER* 1.3 72.8 - - - +
207B VAL* 1.3 58.5 + - - +
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Residues in contact with VAL 207 (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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151B ALA 3.7 0.5 - - - +
152B ILE* 3.5 2.6 - - - +
153B LEU* 2.8 37.0 + - - +
155B PHE* 4.1 18.2 - - + -
160B ALA* 3.6 37.0 - - + +
163B LEU* 4.1 10.5 - - + -
164B VAL* 4.9 0.7 - - + -
185B VAL* 3.4 32.3 - - + -
186B ASP 3.4 7.4 - - - +
187B HIS* 4.5 8.1 - - + -
188B LEU* 4.4 4.0 - - - -
205B SER 4.8 0.4 - - - +
206B VAL* 1.3 79.6 - - - +
208B ARG* 1.3 66.7 + - - +
209B ILE* 4.1 6.3 - - + -
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Residues in contact with ARG 208 (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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51B LYS* 3.5 39.4 + - - +
150B CYS* 4.6 5.3 - - + +
151B ALA 3.4 4.3 - - - +
152B ILE* 3.8 21.7 - - + +
184B ARG 3.7 0.6 - - - +
185B VAL* 3.2 6.4 - - - -
186B ASP* 2.8 62.0 + - - +
188B LEU* 3.5 27.7 - - + +
207B VAL* 1.3 77.4 - - - +
209B ILE* 1.3 63.9 + - - +
210B GLU* 3.7 33.2 + - + -
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Residues in contact with ILE 209 (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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138B VAL* 4.2 26.0 - - + -
141B LEU* 5.5 2.5 - - + -
142B LEU* 3.8 17.7 - - + -
148B PHE* 3.9 7.4 - - + -
150B CYS* 3.3 3.8 - - - +
151B ALA* 2.8 47.2 + - + +
153B LEU* 3.7 26.0 - - + -
155B PHE* 4.6 0.4 - - + -
163B LEU* 4.5 13.2 - - + -
179B THR* 4.7 5.2 - - + -
183B ALA* 3.6 24.7 - - + -
184B ARG 3.5 2.5 - - - -
185B VAL* 4.3 7.6 - - + -
207B VAL* 4.1 9.4 - - + -
208B ARG* 1.3 79.2 - - - +
210B GLU* 1.3 65.8 + - - +
211B PRO* 4.6 2.0 - - + -
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Residues in contact with GLU 210 (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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149B ARG* 3.9 13.2 - - - +
150B CYS* 3.9 17.3 - - + +
183B ALA* 3.9 2.2 - - - -
184B ARG* 2.6 88.5 + - + +
186B ASP* 5.5 0.2 - - - +
208B ARG* 3.7 27.5 + - + -
209B ILE* 1.3 78.3 - - - +
211B PRO* 1.3 66.9 - - - +
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Residues in contact with PRO 211 (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 LEU 5.4 0.4 - - - +
142B LEU* 4.4 11.4 - - + +
147B PHE* 3.7 25.8 - - + -
148B PHE* 3.4 65.9 - - + +
149B ARG 3.9 4.0 - - - +
182B LEU 3.5 10.3 - - - +
183B ALA* 4.1 4.5 - - + -
184B ARG* 4.2 8.7 + - - -
209B ILE* 4.2 1.1 - - + -
210B GLU* 1.3 85.4 - - - +
212B LYS* 1.3 63.5 + - - +
213B ASN* 3.4 7.1 + - - +
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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