Contacts of the strand formed by residues 183 - 192 (chain G) in PDB entry 5DK3
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91G THR* 5.0 7.1 - - - +
117G THR* 3.7 21.6 + - + +
151G ASP 3.0 24.1 + - - -
152G TYR* 2.8 45.8 + - + +
153G PHE* 3.7 27.4 - + - -
154G PRO* 4.2 0.7 - - + -
155G GLU* 3.8 43.1 - - + +
175G ALA* 4.2 6.3 - - + -
176G VAL 3.3 18.2 - - - -
177G LEU* 3.8 35.5 - - + +
178G GLN* 3.2 3.5 + - - -
182G LEU* 1.3 74.5 - - - +
184G SER* 1.3 63.0 + - - +
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Residues in contact with SER 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F THR* 6.1 0.9 - - - +
148G LEU* 3.8 18.2 - - - +
149G VAL 3.3 13.4 + - - -
150G LYS* 3.8 10.2 - - - +
152G TYR* 3.7 3.5 - - - -
174G PRO 4.5 0.3 - - - +
175G ALA* 3.4 0.3 - - - -
176G VAL* 2.9 37.7 + - - +
178G GLN* 3.7 24.7 + - - -
183G TYR* 1.3 81.0 - - - +
185G LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G LEU* 3.7 4.1 - - - +
149G VAL* 2.7 43.7 + - + +
152G TYR* 3.6 10.3 - - - +
155G GLU* 4.7 2.9 - - - +
157G VAL* 3.4 30.3 - - + +
159G VAL* 4.1 16.8 - - + -
172G THR* 3.9 19.5 - - + -
173G PHE 3.6 20.6 - - - +
174G PRO* 4.2 2.9 - - + +
175G ALA* 3.8 13.9 - - + +
184G SER* 1.3 74.9 + - - +
186G SER* 1.3 75.4 + - - +
187G SER 4.2 0.4 - - - +
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Residues in contact with SER 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F VAL* 4.5 7.5 - - - +
180F SER* 4.2 18.6 + - - -
182F THR* 5.1 2.5 + - - -
131G LEU* 3.7 20.6 - - - +
147G CYS 3.4 5.8 - - - -
148G LEU* 3.5 22.5 - - - +
173G PHE* 3.0 38.3 + - - +
185G LEU* 1.3 77.5 - - - +
187G SER* 1.3 60.9 + - - +
188G VAL* 5.0 2.2 - - - -
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Residues in contact with SER 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 4.2 0.3 - - - +
146G GLY* 3.1 2.6 - - - -
147G CYS* 2.9 36.4 + - - +
149G VAL* 5.7 0.2 - - - -
159G VAL* 3.6 28.9 - - - +
161G TRP* 3.0 25.9 + - - -
170G VAL* 4.0 2.1 - - - +
171G HIS 3.5 5.7 + - - -
172G THR* 2.9 24.3 + - - +
185G LEU* 4.2 0.4 - - - +
186G SER* 1.3 73.7 - - - +
188G VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F PHE* 4.5 9.2 - - + -
137F VAL* 5.9 1.3 - - + -
139F LEU* 3.9 32.5 - - + -
141F ASN* 5.0 0.4 - - - +
180F SER* 5.6 1.6 - - - +
131G LEU* 4.4 17.0 - - + -
145G LEU 3.4 12.1 - - - +
146G GLY* 4.1 0.2 - - - -
161G TRP* 4.7 0.9 - - - -
170G VAL* 3.4 6.6 - - - +
171G HIS* 3.0 53.3 + - + +
173G PHE* 3.8 22.2 - - + -
186G SER* 5.0 2.7 - - - -
187G SER* 1.3 81.0 + - - +
189G VAL* 1.3 67.3 + - - +
190G THR* 6.2 1.1 - - + -
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Residues in contact with VAL 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143G ALA 3.9 0.9 - - - +
144G ALA* 3.5 1.6 - - - -
145G LEU* 2.8 61.9 + - + +
161G TRP* 4.1 19.5 - - + -
166G LEU* 3.7 21.3 - - + -
168G SER 3.8 12.8 - - - +
169G GLY 3.4 6.3 - - - -
170G VAL* 3.7 26.5 - - + -
188G VAL* 1.3 78.1 - - - +
190G THR* 1.4 69.5 + - - +
191G VAL* 3.9 6.6 + - + -
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Residues in contact with THR 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F PHE* 4.3 14.8 - - + -
139F LEU* 5.1 2.0 - - + -
141F ASN* 3.4 29.9 + - - +
142F ASN* 5.4 2.4 + - - -
142G THR* 3.9 17.7 - - + +
143G ALA 3.5 2.7 - - - -
144G ALA* 4.2 18.4 - - + -
166G LEU* 5.7 0.2 - - - +
168G SER 4.5 2.3 - - - +
169G GLY* 3.3 26.1 + - - +
188G VAL* 6.2 0.9 - - + -
189G VAL* 1.4 78.1 - - - +
191G VAL* 1.3 63.5 + - - +
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Residues in contact with VAL 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G THR* 3.6 7.0 - - - +
143G ALA 2.9 39.5 + - - +
145G LEU* 4.0 14.4 - - + -
166G LEU* 4.4 5.6 - - + -
189G VAL* 4.0 23.6 - - + -
190G THR* 1.3 79.0 - - - +
192G PRO* 1.4 76.4 - - + +
196G LEU* 3.9 26.2 - - + -
201G TYR* 3.7 32.5 - - + +
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Residues in contact with PRO 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G SER 3.5 10.3 - - - +
142G THR* 4.7 2.0 - - - +
191G VAL* 1.4 92.3 - - + +
193G SER* 1.3 64.7 + - - +
194G SER* 3.1 12.1 - - - +
195G SER* 3.0 35.9 + - - +
196G LEU 4.0 2.4 + - - -
201G TYR* 4.4 2.5 - - - +
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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