Contacts of the strand formed by residues 203 - 207 (chain B) in PDB entry 2Q9Q
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 GLN 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LYS* 3.3 5.4 - - - -
145A LEU* 2.7 55.1 + - + +
146A ASP* 2.9 13.1 + - - +
148A LEU 3.2 22.2 + - - +
150A LEU 5.7 1.2 + - - -
153A ILE* 3.5 20.2 - - + +
173B LEU 3.1 10.5 - - - +
174B ARG* 3.0 42.2 + - + +
201B GLY 4.3 0.2 - - - +
202B SER* 1.3 77.6 - - - +
204B HIS* 1.3 65.0 + - - +
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Residues in contact with HIS 204 (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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142A HIS* 2.9 31.4 + + + +
143A ALA 3.1 7.0 + - - +
144A LYS* 3.8 23.9 - - + -
145A LEU* 3.7 5.1 - - - +
171B VAL 3.7 0.6 - - - +
172B PHE* 3.2 9.7 - - - +
173B LEU* 3.0 45.1 + - + +
175B VAL* 3.9 10.3 - - + -
196B ILE* 5.6 0.7 - - + -
197B ASP 4.5 8.5 - - - -
198B LEU* 3.7 31.0 - - + +
199B GLU 5.2 0.2 - - - -
202B SER* 2.8 29.0 + - - -
203B GLN* 1.3 81.5 + - - +
205B LEU* 1.3 63.5 + - - +
206B ILE* 5.2 2.5 - - + -
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Residues in contact with LEU 205 (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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135A PHE* 4.2 18.8 - - + -
142A HIS* 3.3 6.1 + - - -
143A ALA* 2.7 36.2 + - + +
145A LEU* 4.0 11.0 - - + -
160A LEU* 4.0 20.4 - - + -
161A THR* 4.1 4.5 - - + -
164A LEU* 3.8 23.6 - - + -
170B TYR* 4.1 20.9 - - + -
171B VAL 3.3 18.8 - - - +
172B PHE* 4.0 25.8 - - + -
204B HIS* 1.3 74.4 - - - +
206B ILE* 1.3 68.7 + - - +
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Residues in contact with ILE 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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141A ALA 4.0 12.8 - - - +
142A HIS* 4.3 9.6 - - + +
170B TYR* 3.5 12.1 - - - -
171B VAL* 2.9 32.0 + - + +
173B LEU* 4.3 12.1 - - + -
182B ILE* 5.3 4.0 - - + -
184B VAL* 4.0 28.5 - - + -
196B ILE* 5.9 1.3 - - + -
198B LEU* 6.3 2.9 - - + -
204B HIS* 5.2 2.9 - - + -
205B LEU* 1.3 81.1 - - - +
207B ARG* 1.3 81.9 + - + +
210B THR* 3.9 25.8 - - + +
211B ILE* 4.2 25.4 - - + -
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Residues in contact with ARG 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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141A ALA 4.6 0.2 + - - -
168A TYR* 3.6 34.4 + - - -
168B ASP* 2.9 43.6 + - - +
169B SER 3.7 3.1 - - - -
170B TYR* 3.7 31.9 + - + -
185B GLU* 3.1 49.5 + - - +
187B ASP 5.2 0.6 + - - -
206B ILE* 1.3 83.9 - - + +
208B TYR* 1.3 66.1 + - - +
209B LYS* 3.8 25.0 - - - +
210B THR* 3.2 34.1 + - - +
211B ILE* 3.8 3.1 + - - +
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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