Contacts of the strand formed by residues 176 - 184 (chain I) in PDB entry 4DKE
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 176 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I THR* 5.7 4.5 - - + +
144I ASP 3.1 22.0 + - - -
145I TYR* 2.8 49.1 + + + +
146I PHE* 3.6 36.3 - + - -
147I PRO* 4.6 4.7 - - + -
148I GLU* 4.0 24.2 - - + -
168I ALA* 3.9 20.4 - - + -
169I VAL* 3.7 3.8 - - - -
170I LEU* 3.7 37.9 - - + +
175I LEU* 1.3 73.7 - - - +
177I SER* 1.3 59.2 + - - +
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Residues in contact with SER 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I LEU* 3.9 14.6 - - - +
142I VAL 3.4 12.9 + - - -
143I LYS* 4.1 6.0 - - - +
145I TYR* 4.4 2.0 - - - -
167I PRO 4.8 0.2 - - - +
168I ALA* 3.7 0.6 - - - -
169I VAL* 3.1 29.7 + - - +
171I GLN* 3.2 34.8 + - - -
176I TYR* 1.3 77.3 - - - +
178I LEU* 1.3 68.5 + - - +
160M GLN* 5.7 0.4 - - - -
178M THR* 6.1 1.2 - - - +
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Residues in contact with LEU 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I LEU* 3.8 2.0 - - - +
142I VAL* 2.8 45.8 + - + +
145I TYR* 3.2 28.9 - - + +
148I GLU* 4.7 3.1 - - - +
150I VAL* 4.5 15.9 - - + +
152I VAL* 4.7 6.5 - - + -
165I THR* 3.9 17.3 - - + -
166I PHE* 3.6 24.5 - - + +
167I PRO 4.3 2.2 - - - +
168I ALA* 4.0 13.2 - - + +
177I SER* 1.3 78.9 + - - +
179I SER* 1.3 94.0 + - - +
180I SER 4.1 1.1 - - - +
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Residues in contact with SER 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.1 15.5 - - - +
140I CYS 3.3 11.4 - - - -
141I LEU* 3.9 16.3 - - - +
166I PHE* 3.1 42.2 + - - +
178I LEU* 1.3 86.2 + - - +
180I SER* 1.3 62.1 + - - +
181I VAL* 4.9 2.9 - - - -
133M VAL* 4.7 11.4 - - - +
176M SER* 5.0 8.2 - - - -
178M THR* 4.9 4.7 + - - -
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Residues in contact with SER 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.3 0.7 - - - +
140I CYS* 3.1 32.6 + - - +
142I VAL* 5.3 0.8 - - - +
152I VAL* 3.5 27.9 - - - +
154I TRP* 3.1 23.4 + - - -
163I VAL* 3.8 4.2 - - - +
164I HIS 3.6 4.0 - - - -
165I THR* 3.2 26.2 + - - +
178I LEU* 4.1 1.4 - - - +
179I SER* 1.3 73.6 - - - +
181I VAL* 1.3 70.2 + - - +
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Residues in contact with VAL 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 4.4 15.3 - - + -
137I ALA* 5.1 2.7 - - + -
138I LEU 3.5 14.4 - - - +
139I GLY* 4.2 0.7 - - - -
154I TRP* 4.7 1.6 - - - -
162I GLY 5.5 0.4 - - - +
163I VAL* 3.2 6.7 - - - +
164I HIS* 2.7 42.3 + - + +
166I PHE* 4.2 17.9 - - + -
179I SER* 4.9 2.7 - - - -
180I SER* 1.3 84.3 + - - +
182I VAL* 1.3 70.8 + - - +
183I THR* 5.3 2.7 - - + -
118M PHE* 5.4 4.7 - - + -
133M VAL* 6.0 2.2 - - + -
135M LEU* 3.6 34.5 - - + -
137M ASN* 5.0 5.8 - - - +
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Residues in contact with VAL 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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136I ALA 4.0 0.2 - - - +
137I ALA* 3.7 1.0 - - - -
138I LEU* 2.9 61.7 + - + +
154I TRP* 4.2 16.2 - - + -
159I LEU* 4.0 20.0 - - + -
161I SER 3.9 5.8 - - - +
162I GLY 3.5 15.5 - - - +
163I VAL* 3.8 21.5 - - + -
181I VAL* 1.3 80.5 - - - +
183I THR* 1.3 81.0 + - - +
184I VAL* 4.9 3.8 - - + -
194I TYR* 5.9 0.4 - - + -
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Residues in contact with THR 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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135I THR* 5.2 9.4 - - - -
136I ALA 3.3 11.0 - - - +
137I ALA* 4.4 13.2 - - + -
159I LEU* 5.8 0.3 - - - +
161I SER 4.5 4.9 - - - +
162I GLY* 3.5 16.4 + - - +
181I VAL* 5.3 3.4 - - + -
182I VAL* 1.3 88.9 - - - +
184I VAL* 1.3 66.3 + - - +
116M PHE* 5.1 7.2 - - + -
137M ASN* 3.6 30.3 + - - +
138M ASN* 5.6 1.9 + - - -
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Residues in contact with VAL 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I THR* 4.2 6.6 - - - -
136I ALA* 3.0 28.3 + - - +
138I LEU* 4.5 10.8 - - + -
159I LEU* 5.5 9.9 - - + -
182I VAL* 4.9 6.7 - - + +
183I THR* 1.3 79.2 - - - +
185I PRO* 1.4 93.3 - - + +
186I SER* 4.2 0.2 - - - -
188I SER* 4.9 0.7 - - - +
189I LEU* 4.2 6.7 - - + -
194I TYR* 3.1 51.6 - - + +
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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