Contacts of the strand formed by residues 201 - 207 (chain B) in PDB entry 2ZUQ
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 201 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B VAL* 6.0 1.1 - - - -
159B CYS 3.7 7.2 - - - -
160B PHE* 3.6 20.9 - - - -
185B LEU 3.7 2.4 - - - +
186B ASN* 3.3 4.3 - - - -
187B SER* 3.1 23.6 + - - -
200B MET* 1.3 84.3 - - - +
202B SER* 1.3 62.1 + - - +
203B THR* 4.5 3.4 + - - -
172C PHE* 3.2 16.2 - - - +
184C SER* 2.7 30.2 + - - -
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Residues in contact with SER 202 (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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158B VAL* 3.3 6.9 - - - +
159B CYS* 3.2 31.8 + - - -
171B VAL* 4.4 13.0 + - - -
173B TRP* 2.6 34.7 + - - -
184B VAL* 3.3 6.9 - - - +
186B ASN* 3.1 26.3 + - - -
200B MET* 3.3 12.8 - - - +
201B SER* 1.3 72.1 - - - +
203B THR* 1.3 62.2 + - - +
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Residues in contact with THR 203 (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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156B SER* 4.5 9.2 - - - -
157B VAL 3.7 2.5 - - - -
158B VAL* 3.1 27.2 - - + +
183B GLY 3.4 2.8 - - - +
184B VAL* 3.3 5.7 - - - -
185B LEU* 3.1 37.5 + - - +
201B SER* 4.5 3.3 + - - -
202B SER* 1.3 77.6 + - - +
204B LEU* 1.3 69.5 + - - +
205B THR* 3.7 15.1 + - + +
147C LEU* 4.4 11.5 - - + +
149C LYS* 6.2 0.9 - - - +
182C THR* 5.5 10.5 - - + +
184C SER* 5.0 5.7 - - - -
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Residues in contact with LEU 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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156B SER* 3.4 2.4 - - - -
157B VAL* 2.7 52.5 + - + +
173B TRP* 3.6 50.6 - - + -
175B ILE* 4.3 17.7 - - + -
180B ARG* 4.6 20.4 - - - +
182B ASN 5.9 0.2 - - - +
183B GLY 3.5 4.9 - - - +
184B VAL* 3.6 15.7 - - + -
203B THR* 1.3 72.6 - - - +
205B THR* 1.3 61.7 + - - +
206B LEU* 4.1 30.6 + - + -
217B TYR* 5.9 2.7 - - + -
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Residues in contact with THR 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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155B ALA 4.0 2.7 - - - -
156B SER* 3.7 11.9 + - - -
182B ASN 5.5 0.7 - - - +
183B GLY* 3.2 27.3 + - - +
185B LEU* 5.4 10.8 - - + -
203B THR* 4.2 15.7 - - + +
204B LEU* 1.3 78.1 - - - +
206B LEU* 1.3 64.2 + - - +
149C LYS* 3.6 23.5 + - - +
177C GLN* 6.4 1.1 - - + -
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Residues in contact with LEU 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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154B GLY* 4.8 1.6 - - - -
155B ALA 2.9 23.5 + - - +
157B VAL* 5.9 3.6 - - + -
175B ILE* 6.1 1.3 - - + -
180B ARG* 4.2 20.6 - - - +
204B LEU* 4.1 24.7 + - + -
205B THR* 1.3 80.3 + - - +
207B THR* 1.3 70.4 + - - +
210B GLU* 3.3 38.1 - - + +
211B TYR* 3.9 27.6 - - + -
213B ARG* 3.9 10.5 - - - +
217B TYR* 4.3 14.8 - - + +
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Residues in contact with THR 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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153B GLY 5.3 1.1 - - - -
154B GLY* 5.0 1.3 - - - -
155B ALA* 3.7 7.7 - - - +
206B LEU* 1.3 90.1 - - - +
208B LYS* 1.3 65.8 + - - +
209B ASP* 3.3 6.4 + - - +
210B GLU* 3.2 48.4 + - - +
211B TYR 3.6 7.8 + - - -
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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