Contacts of the strand formed by residues 179 - 185 (chain L) in PDB entry 1FSK
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 179 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120L LYS 5.1 0.9 - - - +
122L THR* 3.2 31.4 - - + +
149L GLY* 3.5 29.4 - - - +
150L TYR 3.6 3.8 - - - +
151L PHE* 3.7 11.4 - - + -
174L VAL 3.7 0.2 - - - +
175L LEU* 3.3 5.9 - - - +
176L GLN* 2.6 44.7 + - + +
177L SER 4.3 4.3 - - - +
178L ASP* 1.3 92.4 - - + +
180L TYR* 1.3 63.9 + - - +
181L THR* 3.7 1.3 - - + +
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Residues in contact with TYR 180 (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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115L THR* 5.2 6.5 - - + +
149L GLY 3.0 22.7 + - - -
150L TYR* 2.8 42.6 + - + +
151L PHE* 3.5 36.6 - + - -
152L PRO 4.4 0.7 - - - -
153L GLU* 3.5 49.4 - - + +
173L ALA* 4.0 8.1 - - + -
174L VAL* 3.1 19.1 - - - -
175L LEU* 3.7 25.8 - - + +
179L LEU* 1.3 69.9 - - - +
181L THR* 1.3 65.6 + - - +
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Residues in contact with THR 181 (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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160K LEU* 5.5 2.9 - - + -
146L LEU* 5.2 5.0 - - - +
147L VAL 3.2 13.5 + - - -
148L LYS* 3.8 34.0 + - + +
149L GLY* 3.9 3.6 - - - +
150L TYR* 3.6 2.0 - - - -
173L ALA* 3.6 1.2 - - - -
174L VAL* 3.1 50.7 + - + +
176L GLN* 4.3 11.0 - - + -
179L LEU 3.7 7.9 - - - +
180L TYR* 1.3 82.8 - - - +
182L LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 182 (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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146L LEU* 3.6 2.4 - - - +
147L VAL* 2.7 54.7 + - + +
150L TYR* 3.8 18.5 - - - +
153L GLU* 5.6 0.9 - - - +
155L VAL* 4.2 19.3 - - + +
157L VAL* 4.5 7.9 - - + -
170L THR* 3.9 18.8 - - + -
171L PHE* 3.3 21.8 - - - +
172L PRO* 5.0 1.3 - - + -
173L ALA* 3.6 15.7 - - + +
181L THR* 1.3 77.4 + - - +
183L SER* 1.3 75.7 + - - +
184L SER 4.3 1.3 - - - +
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Residues in contact with SER 183 (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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133K VAL* 5.6 4.3 - - - -
135K PHE* 4.2 14.4 - - - -
176K SER* 3.2 26.0 + - - -
178K THR* 5.1 5.7 - - - +
129L LEU* 5.5 0.7 - - - -
145L CYS 3.7 7.0 - - - -
146L LEU* 4.0 17.7 - - - -
171L PHE* 2.9 33.5 + - - +
182L LEU* 1.3 83.0 - - - +
184L SER* 1.3 60.8 + - - +
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Residues in contact with SER 184 (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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135K PHE* 4.3 3.8 - - - -
144L GLY* 3.0 2.4 - - - -
145L CYS* 2.9 36.2 + - - +
157L VAL* 3.7 17.3 - - - +
159L TRP* 3.1 24.0 + - - -
168L VAL* 5.0 0.3 - - - +
169L HIS 3.2 8.1 + - - -
170L THR* 2.9 27.9 + - - -
171L PHE* 4.7 0.2 - - - -
182L LEU* 4.3 1.9 - - - +
183L SER* 1.3 75.6 - - - +
185L SER* 1.3 63.1 + - - +
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Residues in contact with SER 185 (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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135K PHE* 3.3 38.1 - - - -
137K ASN* 3.2 22.0 + - - -
142L THR* 5.7 0.7 - - - -
143L LEU 3.4 8.1 - - - -
144L GLY* 3.6 0.4 - - - -
159L TRP* 4.1 0.2 + - - -
167L GLY 5.0 0.9 + - - -
168L VAL* 3.2 4.5 - - - +
169L HIS* 2.8 41.6 + - - +
171L PHE* 4.5 1.6 - - - -
184L SER* 1.3 75.5 + - - +
186L VAL* 1.3 68.9 + - - +
187L THR* 5.1 0.2 + - - -
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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