Contacts of the strand formed by residues 179 - 185 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I LYS 5.1 0.7 - - - +
122I THR* 3.2 31.0 - - + +
149I GLY* 3.5 28.5 - - - +
150I TYR 3.6 3.6 - - - +
151I PHE* 3.7 11.7 - - + -
175I LEU* 3.3 6.4 - - - +
176I GLN* 2.6 44.8 + - + +
177I SER 4.3 3.8 - - - +
178I ASP* 1.3 92.3 - - + +
180I TYR* 1.3 64.1 + - - +
181I THR* 3.7 1.3 - - + +
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Residues in contact with TYR 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I THR* 5.2 6.8 - - + +
149I GLY 3.0 23.0 + - - -
150I TYR* 2.8 42.8 + - + +
151I PHE* 3.5 36.2 - + - -
152I PRO* 4.4 0.7 - - + -
153I GLU* 3.5 50.4 - - + +
173I ALA* 4.0 7.9 - - + -
174I VAL 3.1 18.8 - - - -
175I LEU* 3.7 25.4 - - + +
179I LEU* 1.3 69.8 - - - +
181I THR* 1.3 65.9 + - - +
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Residues in contact with THR 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H LEU* 6.0 1.6 - - + -
146I LEU* 5.2 5.4 - - - +
147I VAL 3.2 13.4 + - - -
148I LYS* 3.8 33.5 + - + +
149I GLY 3.9 3.1 - - - +
150I TYR* 3.6 2.0 - - - -
172I PRO 4.8 0.3 - - - +
173I ALA* 3.6 0.8 - - - -
174I VAL* 3.1 49.6 + - + +
176I GLN* 4.3 11.0 - - + -
179I LEU* 3.7 8.3 - - + +
180I TYR* 1.3 83.6 - - - +
182I LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 3.6 2.2 - - - +
147I VAL* 2.7 54.3 + - + +
150I TYR* 3.8 18.1 - - - +
153I GLU* 5.6 1.3 - - - +
155I VAL* 4.2 20.0 - - + +
157I VAL* 4.5 7.4 - - + -
170I THR* 3.9 19.7 - - + -
171I PHE* 3.3 21.5 - - - +
172I PRO 5.0 1.3 - - - -
173I ALA* 3.6 16.4 - - + +
181I THR* 1.3 76.6 + - - +
183I SER* 1.3 75.6 + - - +
184I SER* 4.3 1.3 - - - +
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Residues in contact with SER 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H VAL* 5.7 4.5 - - - -
135H PHE* 4.4 14.2 - - - -
176H SER* 3.6 21.1 + - - -
129I LEU* 5.5 1.3 - - - -
145I CYS 3.7 6.7 - - - -
146I LEU* 4.0 17.0 - - - +
171I PHE* 2.9 35.9 + - - +
182I LEU* 1.3 83.6 - - - +
184I SER* 1.3 61.9 + - - +
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Residues in contact with SER 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PHE* 4.5 3.8 - - - -
144I GLY* 2.9 2.6 - - - -
145I CYS* 2.9 37.3 + - - +
147I VAL* 6.3 0.2 - - - +
157I VAL* 3.7 17.1 - - - +
159I TRP* 3.1 24.0 + - - -
168I VAL* 5.0 0.5 - - - +
169I HIS 3.2 8.0 + - - -
170I THR* 2.9 29.1 + - - -
182I LEU* 4.3 2.0 - - - +
183I SER* 1.3 75.3 - - - +
185I SER* 1.3 63.4 + - - +
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Residues in contact with SER 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PHE* 3.3 37.9 - - - -
137H ASN* 3.4 20.9 + - - -
142I THR* 5.7 0.2 - - - -
143I LEU 3.4 7.9 - - - -
144I GLY* 3.6 0.7 - - - -
167I GLY 4.9 0.9 + - - -
168I VAL* 3.2 5.1 - - - +
169I HIS* 2.8 42.3 + - - +
171I PHE* 4.5 1.5 - - - -
184I SER* 1.3 76.0 + - - +
186I VAL* 1.3 70.5 + - - +
187I THR* 5.1 0.3 + - - -
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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