Contacts of the strand formed by residues 199 - 204 (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 LEU 199 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184A ARG* 6.1 0.7 - - - +
183C GLY 4.0 3.1 - - - +
184C GLN* 3.8 8.1 - - - -
185C GLU* 3.6 42.2 - - + +
192C SER* 4.5 5.0 - - - +
195C CYS* 3.9 16.1 - - + +
196C ALA* 3.5 36.0 - - + +
197C SER 3.3 4.7 + - - +
198C GLY* 1.3 85.9 - - - +
200C CYS* 1.3 61.6 + - - +
210C CYS* 4.1 6.7 - - + -
211C LYS 3.3 7.6 - - - +
212C PRO* 3.6 26.7 - - + -
213C VAL* 4.1 7.0 - - - +
238C TYR* 4.6 4.2 + - - -
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Residues in contact with CYS 200 (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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201B ASP* 5.6 0.7 - - - -
192C SER* 3.6 14.1 - - - +
195C CYS* 4.0 5.8 - - - -
199C LEU* 1.3 74.7 - - - +
201C CYS* 1.3 68.8 + - - +
202C ALA* 3.5 3.8 + - - -
210C CYS* 3.5 0.5 - - - -
211C LYS 2.7 36.7 + - - +
213C VAL* 4.3 1.3 - - + +
235C GLN* 5.7 2.2 - - - -
236C ARG 5.1 0.2 - - - -
237C CYS* 2.0 52.1 - - + -
238C TYR* 4.0 28.9 - - + +
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Residues in contact with CYS 201 (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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201B ASP* 4.0 10.6 - - - +
189C CYS* 2.0 63.5 - - - -
190C LEU 3.6 15.7 - - - +
191C ARG 3.3 22.9 - - - +
192C SER* 2.9 12.4 + - - +
195C CYS* 3.9 0.9 - - - -
200C CYS* 1.3 72.7 - - - +
202C ALA* 1.3 58.7 + - - +
208C LYS* 3.6 22.6 + - - +
235C GLN* 4.6 4.0 + - - -
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Residues in contact with ALA 202 (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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200C CYS* 3.5 13.6 + - - -
201C CYS* 1.3 75.8 - - - +
203C ARG* 1.3 63.3 + - - +
204C HIS 3.7 0.7 + - - -
208C LYS* 3.8 4.9 - - - -
209C ILE 3.0 30.3 + - - +
211C LYS* 3.8 15.0 - - + -
235C GLN* 3.4 42.0 - - + +
236C ARG 4.3 2.7 - - - +
237C CYS* 4.4 1.8 - - - -
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Residues in contact with ARG 203 (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 5.2 1.6 + - - -
188B SER* 4.5 20.6 + - - +
189B VAL* 4.6 13.9 - - - +
191B PHE* 4.1 28.8 - - + -
202C ALA* 1.3 72.6 - - - +
204C HIS* 1.3 59.3 + - - +
205C PHE 5.3 4.0 - - - +
207C SER 3.7 3.6 - - - +
208C LYS* 3.6 35.0 - - + +
211C LYS* 3.2 3.4 + - - -
229C HIS* 3.0 39.2 + - - -
230C GLY 4.5 4.6 + - - -
232C GLU* 2.6 27.7 + - - +
233C ILE* 3.1 12.2 - - - +
235C GLN* 2.9 60.1 + - + +
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Residues in contact with HIS 204 (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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706A TYR* 3.9 28.4 + + - +
708A GLU* 2.8 30.9 + - - -
724A THR* 4.2 5.6 + - - -
767A TRP* 5.5 5.8 - + - -
202C ALA 3.7 1.2 + - - -
203C ARG* 1.3 71.0 - - - +
205C PHE* 1.3 88.9 - + - +
206C TRP 3.2 1.6 + - - -
207C SER* 2.9 26.1 + - - +
209C ILE* 3.8 26.0 - - + -
211C LYS* 3.5 19.7 + - - +
233C ILE 3.2 1.3 - - - -
234C PHE* 3.5 23.5 - + + -
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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