Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 5KJH
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 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ALA* 4.1 9.9 - - + -
156A SER 3.2 9.9 - - - +
157A ALA* 3.7 22.4 - - + -
162A THR* 1.4 71.7 - - - +
164A ARG* 1.3 70.3 + - - +
165A ILE* 3.9 12.3 - - + -
179A CYS 4.0 0.2 - - - +
180A ILE* 3.5 5.5 - - - +
181A LEU* 2.8 64.5 + - + +
186A HIS* 5.6 0.7 - - + -
190A LEU* 3.5 26.2 - - + -
193A VAL* 3.7 20.6 - - + -
204A SER* 3.8 19.1 - - - +
214A TRP* 5.1 1.1 - - + +
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Residues in contact with ARG 164 (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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136A GLY* 3.7 16.6 + - - -
137A HIS* 3.5 31.5 + - + +
155A ALA* 3.4 4.5 - - - -
156A SER* 3.0 31.6 + - - -
162A THR* 4.3 5.0 + - - +
163A ILE* 1.3 75.9 - - - +
165A ILE* 1.3 61.9 + - - +
166A TRP* 3.7 33.8 - - + +
177A CYS* 3.3 29.2 - - - +
179A CYS 3.5 2.9 - - - -
180A ILE* 3.6 21.3 - - + +
303B TYR* 3.7 23.4 + - - -
306B HIS* 5.6 0.4 + - - -
2564B LEU 3.3 21.6 + - - -
2565B SER 3.5 19.2 + - - -
2566B LYS* 3.9 12.3 - - - +
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Residues in contact with ILE 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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153A ILE* 3.6 28.7 - - + -
154A ILE 3.5 2.5 - - - +
155A ALA* 3.6 26.0 - - + -
163A ILE* 3.9 14.4 - - + -
164A ARG* 1.3 72.9 - - - +
166A TRP* 1.3 59.2 + - - +
177A CYS* 3.5 4.2 - - - -
178A VAL* 2.8 44.1 + - + -
179A CYS* 2.7 36.8 + - + +
181A LEU* 4.4 4.9 - - + -
195A PHE* 4.4 7.4 - - + -
202A VAL* 4.4 6.1 - - + -
216A LEU* 4.2 22.2 - - + -
219A PHE* 4.2 8.3 - - + -
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Residues in contact with TRP 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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118A GLY 6.2 0.2 - - - -
120A VAL* 4.2 6.0 - - + +
134A LEU* 3.9 45.3 - - + -
135A VAL 3.3 36.6 - - - -
136A GLY* 4.1 1.1 - - - -
137A HIS* 4.1 11.7 - + - -
152A TYR 3.5 1.1 - - - +
153A ILE* 3.2 8.7 - - - +
154A ILE* 2.8 58.1 + - + +
156A SER* 2.8 26.6 + - - -
164A ARG* 3.7 37.4 - - + +
165A ILE* 1.3 75.6 - - - +
167A SER* 1.3 61.2 - - - +
168A LEU* 5.8 0.2 - - + -
176A PRO* 3.1 20.6 - - + +
177A CYS* 3.8 30.5 - - + -
178A VAL* 4.5 4.3 - - - -
2565B SER 5.9 0.2 - - - -
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Residues in contact with SER 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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132A ARG* 4.5 1.2 + - - -
150A ASN* 5.8 0.9 + - - -
152A TYR* 3.3 6.6 + - - +
153A ILE* 3.9 15.4 - - - +
166A TRP* 1.3 75.7 - - - +
168A LEU* 1.4 62.2 + - - +
169A ALA* 3.2 18.3 + - - +
172A HIS* 3.0 37.7 + - - +
176A PRO* 2.9 31.1 + - - +
178A VAL* 3.7 14.1 - - - +
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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