Contacts of the strand formed by residues 177 - 186 (chain A) 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 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 5.6 1.0 - - - -
109A GLU* 5.1 11.4 - - - +
142A ASN* 3.2 5.6 + - - -
143A PHE* 2.8 59.5 + - + +
144A TYR* 3.7 27.1 - + - -
145A PRO 4.2 0.2 - - - -
146A ARG* 3.7 51.8 - - + +
167A VAL* 4.3 6.3 - - + -
168A THR* 3.5 23.1 - - - -
169A GLU* 5.0 0.2 - - - -
170A GLN* 3.8 44.0 + - + +
175A SER 4.3 3.4 - - - -
176A THR* 1.3 73.4 - - - +
178A SER* 1.3 62.3 + - - +
171B HIS* 6.0 0.4 - - - -
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.8 0.2 - - - -
140A LEU 3.2 11.7 - - - -
141A ASN* 3.2 15.0 + - - -
142A ASN* 3.0 22.2 + - - -
143A PHE* 3.7 2.5 - - - -
167A VAL* 3.4 6.2 - - - +
168A THR* 2.9 37.1 + - - -
177A TYR* 1.3 70.8 + - - +
179A LEU* 1.3 61.2 + - - +
171B HIS* 3.4 19.0 + - - -
173B PHE* 3.5 17.7 - - - -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 3.6 4.0 - - - +
140A LEU* 2.8 42.0 + - + +
143A PHE* 3.8 16.2 - - + -
146A ARG 5.4 2.2 - - - +
148A ALA* 4.5 23.6 - - + +
150A VAL* 3.9 17.9 - - + -
165A GLU* 3.6 38.8 - - + +
166A SER 3.3 12.3 - - - +
167A VAL* 3.8 17.5 - - + -
178A SER* 1.3 75.6 - - - +
180A SER* 1.4 72.1 + - - +
181A SER 4.0 2.0 - - - +
173B PHE* 3.6 3.6 - - - -
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.6 23.9 - - - +
138A CYS 3.4 5.3 + - - -
139A LEU* 4.7 4.3 - - - +
164A GLN 4.0 0.5 - - - +
165A GLU* 3.3 2.9 - - - -
166A SER* 3.0 33.4 + - - -
179A LEU* 1.4 74.9 - - - +
181A SER* 1.3 57.6 + - - +
182A THR* 5.2 1.8 + - - -
173B PHE* 3.4 31.3 - - - -
186B SER* 4.0 15.5 + - - -
188B VAL* 5.1 2.4 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.4 4.5 - - - +
138A CYS* 2.9 35.6 + - - -
150A VAL* 4.1 18.0 - - - +
152A TRP* 2.9 28.5 + - - -
163A SER* 3.3 11.4 + - - -
164A GLN 3.3 7.3 + - - -
165A GLU* 4.1 15.0 - - - +
179A LEU* 4.0 6.0 - - - +
180A SER* 1.3 75.2 - - - +
182A THR* 1.3 61.5 + - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 3.9 21.8 - - - +
136A VAL 3.3 9.6 - - - +
137A VAL* 3.8 15.0 - - + +
152A TRP* 4.3 2.5 - - - -
163A SER* 3.3 4.9 - - - -
164A GLN* 2.8 36.8 + - - +
180A SER* 5.2 2.8 + - - -
181A SER* 1.3 75.1 + - - +
183A LEU* 1.3 59.8 + - - +
184A THR* 3.8 19.2 + - - +
148B LEU* 4.7 8.9 - - + +
176B VAL* 6.1 2.6 - - - +
186B SER* 4.6 8.3 + - - -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ALA 3.6 1.7 - - - +
135A SER* 3.5 3.3 - - - -
136A VAL* 2.8 46.8 + - + +
152A TRP* 3.7 44.8 - - + +
154A VAL* 3.8 28.0 - - + -
159A GLN* 4.0 11.2 - - + -
162A ASN* 3.4 44.2 - - - +
163A SER* 4.4 1.1 - - - +
182A THR* 1.3 71.0 - - - +
184A THR* 1.3 59.8 + - - +
185A LEU* 4.0 17.9 - - + -
196A TYR* 4.6 2.2 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 3.5 28.3 - - + -
134A ALA 3.6 2.9 - - - +
135A SER* 4.2 5.5 + - - +
162A ASN* 2.8 31.6 + - - +
182A THR* 3.8 17.2 + - - +
183A LEU* 1.3 74.7 + - - +
185A LEU* 1.3 70.9 + - - +
150B LYS* 4.4 12.5 + - - +
178B GLN* 5.5 1.5 + - - +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 3.5 8.0 - - - +
134A ALA* 2.8 38.4 + - + +
136A VAL* 4.7 3.1 - - + -
154A VAL* 4.6 5.6 - - + -
159A GLN* 4.3 6.5 - - - +
162A ASN* 3.7 21.3 - - - +
183A LEU* 4.0 21.8 - - + +
184A THR* 1.3 84.2 - - - +
186A SER* 1.3 68.0 + - - +
189A ASP* 4.7 9.6 - - + +
190A TYR* 4.4 18.6 - - + +
193A HIS* 6.3 0.4 - - + -
196A TYR* 3.7 30.1 - - + -
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLY 3.6 11.4 - - - -
133A THR* 4.4 1.1 - - - +
134A ALA 4.4 0.2 - - - -
185A LEU* 1.3 76.2 - - - +
187A LYS* 1.3 58.5 + - - +
188A ALA* 3.9 8.5 + - - +
189A ASP* 3.1 33.5 + - - +
190A TYR* 2.9 25.5 + - - +
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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