Contacts of the strand formed by residues 183 - 189 (chain B) in PDB entry 1F15
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 TYR 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG* 3.2 6.7 - - - +
90B LEU* 2.8 36.2 + - + -
107B LEU* 4.2 12.1 - - + -
126B ARG* 3.4 11.7 - - - +
127B LYS* 3.6 56.3 + - + +
168B TYR* 4.7 5.6 - + - -
170B LEU* 3.2 48.5 - - + +
173B MET* 5.4 4.5 - - - -
175B ALA* 4.1 8.7 - - + +
179B ASP* 3.3 27.3 - - + +
180B MET* 3.1 17.1 + - + +
181B ARG 4.6 0.2 - - - -
182B LYS* 1.3 86.9 - - + +
184B ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY* 5.4 0.4 - - - -
88B LYS 3.1 26.5 - - - +
89B ARG* 3.8 9.2 - - + +
90B LEU* 4.2 1.8 - - - -
125B VAL* 3.5 4.3 - - - -
126B ARG 2.9 29.8 + - - +
128B VAL* 4.5 19.3 - - + +
183B TYR* 1.3 78.5 - - - +
185B VAL* 1.3 66.4 + - - +
186B LEU* 3.9 10.1 + - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 5.2 7.0 - - + -
86B TYR* 3.8 2.8 - - + +
87B GLY* 3.0 24.9 - - - -
88B LYS* 2.8 15.8 + - + +
90B LEU* 3.9 15.2 - - + +
109B ILE* 3.6 31.6 - - + -
123B VAL* 4.4 8.1 - - + -
124B THR 3.6 7.0 - - - +
125B VAL* 3.7 7.6 - - + -
184B ALA* 1.3 72.9 - - - +
186B LEU* 1.3 72.8 + - - +
187B VAL* 4.0 15.7 - - + -
201B LEU* 4.2 14.6 - - + -
203B VAL* 3.9 10.1 - - + -
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 3.6 31.2 - - + -
86B TYR 3.3 1.6 - - - +
87B GLY* 3.9 10.8 - - - -
88B LYS 5.4 0.2 - - - +
122B TRP 4.3 0.7 - - - -
123B VAL* 3.5 22.2 - - - +
124B THR* 3.2 18.3 + - - +
126B ARG* 4.9 8.3 - - + -
128B VAL* 4.7 11.2 - - + -
139B ILE* 3.7 15.3 - - + +
142B MET* 3.8 35.7 - - + -
143B PHE* 4.8 14.4 - - + -
184B ALA* 4.4 13.0 - - + +
185B VAL* 1.3 76.2 - - - +
187B VAL* 1.3 69.1 + - - +
188B TYR 4.2 0.7 - - - -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 5.5 0.7 - - + -
80B ILE* 3.4 28.6 - - + +
85B TYR* 3.2 4.4 - - - +
86B TYR* 2.8 38.6 + - + +
121B VAL* 4.2 25.6 - - + -
122B TRP 3.6 3.1 - - - -
123B VAL* 4.3 12.1 - - + -
185B VAL* 4.0 7.9 - - + -
186B LEU* 1.3 79.7 - - - +
188B TYR* 1.3 60.8 + - - +
189B SER 3.7 0.2 + - - -
194B LEU* 4.6 4.5 - - + -
199B LEU* 4.9 4.5 - - + -
201B LEU* 3.6 31.0 - - + -
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Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY* 3.3 33.3 + - - -
84B SER 3.3 18.6 - - - -
85B TYR* 3.8 8.9 - - + +
121B VAL* 3.4 5.1 - - - -
122B TRP* 3.1 42.3 + + + +
136B VAL* 6.4 2.0 - - + -
139B ILE* 4.9 1.6 - - + -
140B SER* 4.3 20.2 - - - -
143B PHE* 3.6 29.3 - + + -
186B LEU 4.2 0.4 - - - -
187B VAL* 1.3 72.0 - - - +
189B SER* 1.3 69.7 + - - +
190B LYS* 3.6 27.9 + - + +
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Residues in contact with SER 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.9 13.6 - - - +
81B ASP 3.7 17.0 - - - -
82B ARG* 4.5 1.2 - - - -
83B GLY* 3.0 25.8 + - - -
84B SER 3.1 6.7 + - - -
119B SER* 5.1 1.0 - - - -
120B THR 3.7 7.8 + - - -
121B VAL* 4.7 3.1 - - - +
187B VAL 3.7 3.4 + - - -
188B TYR* 1.3 77.5 - - - +
190B LYS* 1.3 59.9 + - - +
192B ASP* 4.0 5.0 + - - +
193B ALA* 3.3 25.1 + - - -
194B LEU* 3.5 15.8 + - - +
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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