Contacts of the strand formed by residues 142 - 152 (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 THR 142 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120F PHE* 3.7 19.0 - - + -
140G GLU* 3.5 18.5 - - - +
141G SER* 1.4 85.5 + - - +
143G ALA* 1.4 62.3 + - - +
190G THR* 3.9 28.5 - - + -
191G VAL 3.6 13.0 + - - +
192G PRO* 5.0 2.1 - - - +
193G SER* 4.6 1.8 - - - -
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Residues in contact with ALA 143 (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* 4.2 3.8 - - - -
133G PRO* 5.1 4.3 - - + -
136G ARG* 5.1 8.7 - - + -
142G THR* 1.4 73.1 - - - +
144G ALA* 1.3 63.5 + - - +
145G LEU* 6.0 0.7 - - + -
190G THR* 3.5 2.3 - - - -
191G VAL* 2.9 37.6 + - - +
193G SER* 4.1 19.3 - - - +
196G LEU* 4.1 27.1 - - + -
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Residues in contact with ALA 144 (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* 3.5 45.4 - - + -
122F PHE* 3.3 26.1 - - + -
139F LEU* 4.0 10.3 - - + -
133G PRO* 3.5 15.1 - - - +
143G ALA* 1.3 75.7 - - - +
145G LEU* 1.3 63.3 + - - +
188G VAL* 5.6 0.7 - - + -
189G VAL 3.5 6.3 - - - +
190G THR* 4.2 6.1 - - + +
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Residues in contact with LEU 145 (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* 4.2 6.1 - - - -
131G LEU 3.3 12.6 - - - +
132G ALA* 4.9 3.4 - - - -
133G PRO* 5.0 2.2 - - + -
143G ALA 6.0 0.4 - - - -
144G ALA* 1.3 75.4 - - - +
146G GLY* 1.3 59.1 + - - +
161G TRP* 3.7 18.6 - - + -
188G VAL* 3.4 2.9 - - - +
189G VAL* 2.8 67.5 + - + +
191G VAL* 4.0 17.0 - - + -
196G LEU* 4.3 11.7 - - + -
201G TYR* 3.7 38.6 - - + -
218G VAL* 4.0 8.5 - - + -
219G GLU* 4.4 15.0 - - + +
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Residues in contact with GLY 146 (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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130G PRO* 3.6 2.4 - - - +
131G LEU* 2.7 48.9 + - - +
145G LEU* 1.3 76.5 - - - +
147G CYS* 1.3 63.9 + - - -
161G TRP* 3.6 12.6 - - - -
187G SER 3.1 13.7 - - - -
188G VAL* 4.1 0.9 - - - -
218G VAL* 3.8 6.4 - - - +
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Residues in contact with CYS 147 (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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128G VAL* 4.0 13.5 - - + -
129G PHE 3.4 6.5 - - - +
131G LEU* 3.7 5.1 - - - +
146G GLY* 1.3 77.4 - - - -
148G LEU* 1.3 59.2 + - - +
149G VAL* 3.8 9.1 + - + +
159G VAL* 5.3 0.2 - - + -
161G TRP* 4.0 2.5 - - + -
185G LEU 4.1 0.2 - - - +
186G SER* 3.4 2.9 - - - -
187G SER* 2.9 33.4 + - - +
203G CYS* 2.0 52.5 - - + -
205G VAL* 5.0 0.2 - - + -
216G LYS* 4.5 5.8 - - - -
218G VAL* 3.7 15.7 - - - -
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Residues in contact with LEU 148 (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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128F GLN* 4.4 7.4 - - - +
135F SER* 3.5 35.7 - - - +
137F VAL* 4.6 12.1 - - + -
182F THR* 5.2 7.2 - - + +
127G SER 3.5 2.8 - - - +
128G VAL* 3.5 3.9 - - - -
129G PHE* 2.8 48.3 + - + +
131G LEU* 4.0 14.2 - - + +
147G CYS* 1.3 69.4 - - - +
149G VAL* 1.3 61.1 + - - +
150G LYS* 3.6 13.4 + - + -
184G SER* 3.8 20.9 - - - +
185G LEU 3.8 4.5 - - - +
186G SER* 3.5 20.2 - - - +
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Residues in contact with VAL 149 (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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126G PRO* 3.5 25.8 - - + -
127G SER 3.7 3.6 - - - -
128G VAL* 4.6 3.8 - - + +
147G CYS* 4.2 13.0 - - + +
148G LEU* 1.3 71.3 - - - +
150G LYS* 1.3 57.2 + - - +
152G TYR* 3.5 14.7 - - + -
157G VAL* 4.1 8.3 - - + -
159G VAL* 4.3 14.6 - - + -
184G SER* 3.3 5.1 - - - -
185G LEU* 2.7 44.8 + - + +
187G SER 5.5 0.2 - - - +
205G VAL* 3.7 39.9 - - + -
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Residues in contact with LYS 150 (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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128F GLN* 3.7 28.5 - - - +
133F THR* 4.4 14.0 - - - +
135F SER* 3.7 9.0 + - - +
182F THR* 6.3 0.2 - - - +
184F THR* 4.0 24.7 + - - +
126G PRO* 3.5 1.4 - - - +
127G SER* 3.0 37.6 + - - +
129G PHE* 4.4 10.8 - - + -
148G LEU* 3.6 14.8 + - + -
149G VAL* 1.3 74.3 - - - +
151G ASP* 1.4 90.1 + - - +
152G TYR* 3.7 2.2 - - - -
178G GLN* 2.8 26.3 + - - +
184G SER* 3.8 15.9 - - - +
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Residues in contact with ASP 151 (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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133F THR* 5.4 1.4 + - - -
124G LYS* 3.5 25.8 + - - +
125G GLY 3.5 14.4 - - - +
127G SER* 5.1 7.0 + - - +
129G PHE* 6.0 0.9 - - - -
150G LYS* 1.4 98.8 + - - +
152G TYR* 1.3 57.8 + - - +
178G GLN* 3.0 21.1 + - - +
180G SER* 4.7 2.1 + - - -
182G LEU* 3.7 26.5 - - + +
183G TYR 3.0 14.7 + - - -
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Residues in contact with TYR 152 (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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124G LYS 3.3 12.6 - - - +
126G PRO* 3.6 21.5 - - + -
149G VAL* 3.5 43.5 - - + -
151G ASP* 1.3 77.5 - - - +
153G PHE* 1.3 62.9 + - - +
154G PRO 3.6 19.7 - - - -
155G GLU* 3.1 27.9 + - - -
157G VAL* 3.5 31.7 - - + +
175G ALA* 3.2 18.0 - - - +
182G LEU* 3.7 2.6 - - - -
183G TYR* 2.8 45.3 + - + +
184G SER* 3.7 10.3 - - - -
185G LEU* 3.6 5.4 - - - +
207G HIS* 3.8 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