Contacts of the strand formed by residues 162 - 169 (chain A) in PDB entry 4KG8
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 ILE 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.9 33.9 - - + -
161A THR* 1.3 78.1 - - - +
163A THR* 1.3 72.3 + - - +
164A HIS* 4.2 2.9 + - + +
182A SER 3.6 1.0 - - - +
183A GLN* 3.4 2.9 - - - -
184A GLN* 2.8 37.5 + - + +
186A PRO* 4.0 16.4 - - + -
197A TRP* 3.8 29.8 - - + -
219A VAL* 4.2 15.3 - - + -
220A LEU 3.2 10.1 - - - +
221A ASP* 4.7 12.1 - - - +
223A ARG 5.2 5.2 - - - +
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Residues in contact with THR 163 (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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161A THR* 4.5 7.3 + - - +
162A ILE* 1.3 76.2 - - - +
164A HIS* 1.3 58.5 + - - +
165A GLY 4.2 0.4 - - - -
167A TYR* 4.0 14.6 - - - +
181A VAL* 3.6 29.6 - - + -
182A SER 3.2 5.2 - - - +
183A GLN* 4.2 14.1 + - + +
218A ARG 3.9 0.7 - - - +
219A VAL* 3.3 4.7 - - - -
220A LEU* 2.8 48.5 + - + +
232B ARG* 5.0 4.7 - - - +
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 3.1 35.2 + - - -
147A VAL* 3.7 15.0 - - + +
149A LEU* 5.9 0.7 - - + -
162A ILE* 4.1 4.7 + - + -
163A THR* 1.3 73.8 - - - +
165A GLY* 1.3 60.4 + - - +
181A VAL* 4.5 1.3 - - - -
182A SER* 2.8 38.5 + - - +
201A SER* 2.8 49.2 + - - +
203A LEU* 3.2 28.2 - - + +
217A VAL* 3.7 9.1 - - + +
218A ARG 3.5 4.0 - - - -
219A VAL* 3.9 22.9 - - + -
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Residues in contact with GLY 165 (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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163A THR 4.2 0.6 - - - -
164A HIS* 1.3 75.5 - - - +
166A LEU* 1.3 63.0 + - - -
167A TYR* 3.5 22.9 + - - -
180A LEU 3.4 9.0 - - - -
181A VAL* 4.1 2.7 - - - -
203A LEU* 4.0 3.4 - - - -
217A VAL* 3.3 9.4 - - - +
218A ARG 3.0 34.4 + - - +
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Residues in contact with LEU 166 (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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143A ILE* 4.2 18.2 - - + -
144A TYR* 4.0 20.2 - - - +
145A SER* 4.1 5.8 - - - +
165A GLY* 1.3 75.4 - - - +
167A TYR* 1.3 63.1 + - - +
178A GLU* 4.1 0.3 - - - -
179A LEU* 2.9 26.7 + - - +
180A LEU* 2.9 37.7 + - + +
203A LEU* 3.9 23.1 - - + -
215A VAL* 3.9 10.1 - - + -
216A VAL 3.4 1.3 - - - -
217A VAL* 3.7 14.4 - - + -
235A PHE* 3.4 35.4 - - + -
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Residues in contact with TYR 167 (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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163A THR* 4.0 19.4 - - - +
165A GLY* 3.5 37.1 + - - -
166A LEU* 1.3 72.8 - - - +
168A LYS* 1.3 58.7 + - - +
169A ARG 4.3 0.2 + - - -
176A GLU* 3.8 31.0 - - + +
177A LEU 3.2 8.5 - - - +
178A GLU* 3.8 38.8 + - + -
179A LEU* 3.8 5.1 - - - +
181A VAL* 4.1 6.3 - - + +
215A VAL* 3.2 7.1 - - - +
216A VAL* 2.8 39.7 + - + +
218A ARG* 3.8 32.0 + - + -
220A LEU* 4.7 8.9 - - + +
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Residues in contact with LYS 168 (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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167A TYR* 1.3 71.9 - - - +
169A ARG* 1.3 72.9 + - - +
170A THR* 4.6 4.0 - - - -
175A GLU 4.5 0.5 - - - +
176A GLU* 3.6 5.2 - - - -
177A LEU* 2.8 61.7 + - + +
179A LEU* 3.7 25.9 - - + +
208A HIS 4.5 9.9 + - - +
209A LEU* 4.0 17.9 - - + -
213A GLU* 3.9 26.2 + - + +
214A GLU 3.4 7.2 - - - +
215A VAL* 4.6 0.2 - - - +
120B LEU* 4.4 19.0 - - - +
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Residues in contact with ARG 169 (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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110A GLY* 5.6 0.4 - - - -
111A PRO* 3.9 14.5 - - - +
129A HIS* 5.1 3.2 + - - -
130A ASP* 5.2 3.4 + - - +
132A ALA* 4.2 4.2 - - - +
168A LYS* 1.3 72.7 - - - +
170A THR* 1.3 61.6 + - - +
173A TYR 5.7 0.9 - - - +
175A GLU 5.6 0.9 - - - -
176A GLU* 2.8 45.3 + - + +
212A GLY 4.8 0.9 - - - +
213A GLU* 3.5 9.7 - - - +
214A GLU* 2.8 66.2 + - + +
216A VAL* 3.7 28.4 - - + +
218A ARG* 3.9 10.3 - - - +
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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