Contacts of the strand formed by residues 207 - 212 (chain C) in PDB entry 5FWW
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 207 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A TYR* 4.4 11.3 + - - -
140B ASN* 5.2 0.9 - - - -
165B TYR* 4.7 12.3 - - - -
191B PHE* 3.9 6.0 - - - -
188C VAL* 5.5 10.6 - - - +
203C ARG* 3.7 1.7 - - - +
204C HIS* 2.9 34.5 + - - +
205C PHE* 3.7 0.6 - - - +
206C TRP* 1.3 79.4 + - - +
208C LYS* 1.3 66.4 + - - +
209C ILE* 4.8 3.7 - - - +
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Residues in contact with LYS 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B SER* 3.6 46.4 + - - +
165B TYR* 3.6 17.8 + - + +
188B SER* 5.0 3.8 + - - -
200B GLY 4.7 0.2 - - - -
201B ASP* 4.5 17.6 + - - +
188C VAL* 3.5 7.3 - - - +
189C CYS* 3.0 36.7 + - - +
190C LEU 4.0 2.0 + - - +
201C CYS* 3.6 32.4 + - - +
202C ALA* 3.6 3.6 - - - +
203C ARG* 3.6 43.6 - - + +
207C SER* 1.3 72.9 - - - +
209C ILE* 1.3 65.3 + - - +
235C GLN* 5.0 6.0 - - - +
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Residues in contact with ILE 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TYR* 3.6 35.2 - - + +
186C GLY* 3.6 28.0 - - - +
187C SER 3.3 9.9 - - - +
188C VAL* 4.3 11.7 - - + -
189C CYS* 3.5 5.6 - - - -
202C ALA 3.0 25.8 + - - +
204C HIS* 3.8 26.7 - - + -
207C SER* 4.8 6.3 - - - +
208C LYS* 1.3 79.0 - - - +
210C CYS* 1.3 63.6 + - - +
211C LYS* 3.3 24.5 + - + +
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Residues in contact with CYS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C GLY* 4.3 9.0 - - - -
184C GLN 3.3 20.9 - - - +
185C GLU* 3.5 7.4 - - - +
186C GLY* 3.0 23.6 + - - +
187C SER 3.0 14.6 + - - -
189C CYS* 3.7 13.0 - - - -
195C CYS* 2.0 53.2 - - + -
199C LEU* 4.1 8.7 - - + -
200C CYS 3.5 6.5 - - - -
209C ILE* 1.3 69.8 - - - +
211C LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C GLU* 5.1 0.4 - - - -
199C LEU* 3.3 5.0 - - - -
200C CYS 2.7 34.5 + - - +
202C ALA* 3.8 16.6 - - + -
203C ARG 3.2 21.2 + - - -
204C HIS* 3.5 22.5 + - - -
209C ILE* 3.3 26.4 + - + +
210C CYS* 1.3 77.9 - - - +
212C PRO* 1.3 71.6 - - + +
234C PHE 4.1 1.2 - - - -
235C GLN 2.7 32.8 + - - +
236C ARG* 5.2 2.7 - - - -
237C CYS* 3.2 15.3 - - + +
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Residues in contact with PRO 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C GLU* 3.4 28.7 - - + +
198C GLY 3.7 3.4 - - - +
199C LEU* 3.6 17.7 - - + -
211C LYS* 1.3 92.3 - - + +
213C VAL* 1.3 67.9 + - - +
214C LEU* 3.7 9.5 - - + +
237C CYS* 3.5 11.6 + - - +
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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