Contacts of the strand formed by residues 165 - 169 (chain C) in PDB entry 1FZB
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 GLY 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C HIS* 4.3 10.8 - - - -
163C GLN 3.2 5.6 + - - -
164C SER* 1.3 73.7 - - - +
166C LEU* 1.3 62.2 + - - -
167C TYR* 3.1 13.0 - - - -
181C TYR* 3.6 14.5 - - - -
182C CYS 2.9 30.2 + - - -
220C PRO* 3.9 8.7 - - - -
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Residues in contact with LEU 166 (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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203B ILE* 4.4 12.8 - - + -
143C VAL* 5.4 3.1 - - + -
144C GLN 4.6 13.2 + - - +
145C ILE* 4.2 3.4 - - + -
146C HIS* 3.4 24.0 + - - -
165C GLY* 1.3 72.1 - - - -
167C TYR* 1.3 66.5 + - - +
179C LEU* 3.7 30.5 - - + -
180C VAL 3.3 9.6 - - - +
181C TYR* 3.6 13.0 - - + -
218C LEU* 3.9 28.7 - - + +
219C SER 3.1 33.4 - - - +
220C PRO* 3.8 18.4 - - + +
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Residues in contact with TYR 167 (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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145C ILE* 4.6 4.5 - - - -
146C HIS* 3.2 43.0 + + + -
148C ILE* 3.3 37.2 - - + +
156C ILE* 3.6 25.1 - - + -
161C ALA* 3.7 17.1 - - + +
162C LYS* 4.7 1.7 + - - +
163C GLN* 2.7 31.2 + - - +
165C GLY 3.1 32.1 - - - -
166C LEU* 1.3 74.7 - - - +
168C PHE* 1.3 61.4 + - - +
169C ILE* 4.8 0.4 - - + -
178C PHE 3.5 0.3 - - - +
179C LEU* 3.1 11.9 - - - +
180C VAL* 2.9 32.8 + - - +
182C CYS* 3.5 27.1 - - + -
184C ILE* 4.4 1.1 - - + -
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Residues in contact with PHE 168 (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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226B LEU* 4.3 16.2 - - + -
228B GLN* 5.7 1.6 - - - -
234B LYS* 4.8 10.1 - - + +
235B PRO* 3.3 35.4 - - + -
145C ILE* 4.3 24.5 - - + -
146C HIS 4.8 5.4 + - - +
148C ILE 3.9 3.8 + - - +
149C THR* 3.2 33.5 - - - +
167C TYR* 1.3 73.7 - - - +
169C ILE* 1.3 63.7 + - - +
177C GLN* 3.2 38.1 - - + +
178C PHE* 3.2 18.2 - - - -
179C LEU* 3.6 26.0 - - + -
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Residues in contact with ILE 169 (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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149C THR* 4.2 1.1 - - - -
150C GLY 3.1 17.7 - - - +
151C LYS 4.1 12.3 - - - +
152C ASP* 4.2 14.6 - - - -
153C CYS 4.6 0.2 - - - +
156C ILE* 3.8 20.4 - - + -
168C PHE* 1.3 82.1 - - - +
170C LYS* 1.3 59.4 + - - +
171C PRO* 4.1 0.6 - - + +
177C GLN* 3.3 2.6 - - - -
178C PHE* 2.8 55.1 + - + +
180C VAL* 3.5 39.7 - - + -
192C THR* 4.7 3.4 - - - +
236C ILE* 3.7 20.0 - - + -
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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