Contacts of the strand formed by residues 201 - 208 (chain L) in PDB entry 2ZPK
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 HIS 201 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113L SER* 5.1 10.1 + - - -
114L PRO* 6.1 0.4 - - - +
196L VAL 3.7 1.0 - - - +
197L THR* 3.3 1.2 - - - +
198L HIS* 2.8 36.3 + - - +
199L GLU 3.3 4.0 - - - +
200L GLY* 1.3 79.3 - - - +
202L THR* 1.3 91.3 + - - +
203L VAL* 3.7 23.0 + - + +
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Residues in contact with THR 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L GLN* 3.9 31.4 - - + +
196L VAL 3.3 7.2 - - - +
197L THR* 2.9 27.0 + - - +
201L HIS* 1.3 94.5 + - - +
203L VAL* 1.3 64.4 + - - +
204L GLU* 4.1 3.9 + - + +
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Residues in contact with VAL 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L SER* 5.2 3.8 - - - -
114L PRO* 4.1 32.1 - - + +
116L VAL* 3.6 31.4 - - + +
194L CYS 3.8 1.4 - - - +
195L GLN* 3.6 0.5 - - - -
196L VAL* 2.7 38.9 + - - +
201L HIS* 3.7 25.8 - - + +
202L THR* 1.3 73.2 - - - +
204L GLU* 1.3 62.0 + - - +
205L LYS* 4.6 15.5 - - - +
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Residues in contact with GLU 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L SER* 2.3 37.5 + - - +
194L CYS 3.4 3.6 - - - -
195L GLN* 2.5 32.6 + - + -
202L THR* 4.0 5.6 + - + +
203L VAL* 1.3 76.0 - - - +
205L LYS* 1.3 74.1 + - - +
206L SER* 3.8 11.9 + - - +
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Residues in contact with LYS 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116L VAL* 2.6 56.8 + - + +
117L THR* 4.5 1.8 - - - +
118L LEU* 3.7 23.3 - - + +
193L SER* 3.3 2.8 + - - -
194L CYS 2.8 33.1 + - - +
203L VAL* 4.3 11.5 - - - +
204L GLU* 1.3 81.9 - - - +
206L SER* 1.3 64.5 + - - +
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Residues in contact with SER 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L LEU* 3.9 5.9 - - - +
191L SER* 5.9 3.1 - - - -
192L TYR 3.1 11.2 - - - -
193L SER* 3.4 15.9 + - - -
204L GLU* 3.8 11.1 + - - +
205L LYS* 1.3 79.8 + - - +
207L LEU* 1.3 66.8 + - - +
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Residues in contact with LEU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H ARG* 4.5 5.8 - - - +
118L LEU* 3.8 32.1 - - + +
119L PHE 3.9 0.4 - - - -
120L PRO* 3.6 40.8 - - + -
133L LEU* 4.4 3.6 - - + -
186L TRP* 4.0 22.0 - - + -
191L SER* 3.4 4.2 - - - -
192L TYR* 2.9 44.0 + - + +
206L SER* 1.3 76.9 - - - +
208L SER* 1.3 76.5 + - - +
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Residues in contact with SER 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H ARG* 3.2 20.1 + - - -
190L SER* 3.2 12.3 - - - -
191L SER* 4.4 5.6 - - - +
207L LEU* 1.3 78.7 + - - +
209L ARG* 1.3 65.4 + - - +
210L ALA* 3.3 14.5 + - - -
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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