Contacts of the strand formed by residues 160 - 167 (chain K) in PDB entry 5LS6
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 HIS 160 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65J ILE* 4.3 0.4 - - - -
66J GLN* 3.4 21.2 + - - -
154K TYR* 3.1 7.5 - - - +
155K ASP* 2.9 31.7 + - + -
158K THR* 3.1 35.8 + - - +
159K SER* 1.3 77.8 - - - +
161K PRO* 1.3 67.8 - - + +
162K LEU* 4.9 1.1 - - + -
176K ASN* 3.3 40.5 + - - +
178K ILE* 3.9 22.8 - - + +
179K THR* 4.5 6.9 - - - +
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Residues in contact with PRO 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J ILE* 3.7 19.1 - - + +
67J PRO* 3.7 30.3 - - + -
68J VAL 4.9 0.9 - - - +
102K ASN* 4.2 8.1 - - - +
104K HIS* 5.8 0.4 - - + -
152K TRP* 4.1 19.7 - - + -
153K THR 3.6 8.3 - - - +
154K TYR* 4.2 2.7 - - + -
160K HIS* 1.3 87.2 - - + +
162K LEU* 1.3 69.5 + - - +
176K ASN* 3.4 3.8 + - - -
177K PRO* 3.3 23.2 - - + +
178K ILE* 3.8 20.6 - - + -
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Residues in contact with LEU 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K ALA 3.9 0.2 - - - +
152K TRP* 3.4 6.5 - - - -
153K THR* 2.7 58.1 + - + +
154K TYR 3.6 5.4 - - - +
155K ASP* 3.4 36.6 - - + +
160K HIS* 4.3 2.5 - - + +
161K PRO* 1.3 83.3 - - - +
163K LEU* 1.3 59.7 + - - +
174K ILE* 4.2 11.4 - - + -
175K ILE 3.6 14.4 - - - +
176K ASN* 3.8 13.9 - - + +
177K PRO* 4.3 0.7 - - - -
183K ILE* 3.6 31.0 - - + -
184K LYS* 6.6 0.2 - - - -
220K ILE* 4.8 8.5 - - + -
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Residues in contact with LEU 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ALA* 3.3 27.4 - - + -
121K VAL* 3.4 25.6 - - + -
123K LEU* 3.8 11.0 - - + -
138K TYR* 6.4 0.2 - - + -
150K CYS* 3.9 17.5 - - + -
151K ALA 3.7 23.8 - - - +
152K TRP* 3.9 30.7 - - + +
162K LEU* 1.3 73.0 - - - +
164K ALA* 1.3 62.0 + - - +
165K VAL* 4.4 5.2 - - + -
173K ARG 4.0 0.2 - - - +
174K ILE* 3.5 3.6 - - - -
175K ILE* 2.7 51.3 + - + +
177K PRO* 4.6 4.3 - - + +
198K PHE* 5.5 0.2 - - - -
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Residues in contact with ALA 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K CYS* 2.9 28.4 - - - +
151K ALA 3.0 20.4 + - - +
162K LEU 4.2 0.4 + - - -
163K LEU* 1.3 72.2 - - - +
165K VAL* 1.3 61.1 + - - +
172K ILE* 4.9 0.7 - - + -
173K ARG 3.4 5.8 - - - +
174K ILE* 3.7 18.4 - - + -
196K LEU* 3.7 17.2 - - + +
198K PHE* 3.7 19.5 - - + -
206K LEU* 4.2 4.7 - - + -
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Residues in contact with VAL 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU* 5.3 0.2 - - + -
116K VAL* 3.6 24.9 - - + -
121K VAL* 4.0 20.9 - - + -
147K PHE* 3.4 35.4 - - + -
149K THR 3.4 7.4 - - - +
150K CYS* 4.1 4.0 - - + -
163K LEU* 4.1 5.8 + - + -
164K ALA* 1.3 78.4 - - - +
166K ALA* 1.3 66.1 + - - +
172K ILE* 3.5 2.3 - - - -
173K ARG* 2.9 49.4 + - + +
175K ILE* 4.9 11.2 - - + -
196K LEU* 3.6 3.9 - - - +
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Residues in contact with ALA 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K PHE* 3.5 10.7 - - - -
148K TYR 2.8 19.2 + - - -
149K THR* 3.2 13.1 + - + +
165K VAL* 1.3 81.9 - - - +
167K GLY* 1.3 58.4 + - - +
171K ILE 3.4 15.7 - - - +
172K ILE* 4.3 1.8 - - + -
193K ILE* 3.7 31.2 - - + -
196K LEU* 3.5 19.5 - - + -
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Residues in contact with GLY 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K GLU* 3.6 8.0 + - - -
146K ASN 3.4 12.1 - - - -
148K TYR* 3.6 11.9 - - - -
166K ALA* 1.3 77.2 - - - +
168K SER* 1.3 56.5 + - - -
169K ARG 3.2 3.1 - - - -
170K GLY* 2.8 25.1 + - - -
171K ILE 4.1 4.0 + - - +
192K ALA* 4.0 0.2 - - - -
193K ILE* 3.2 24.3 + - - +
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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