Contacts of the strand formed by residues 169 - 176 (chain B) in PDB entry 5LK5
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 THR 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP* 6.0 0.4 - - - +
96B THR* 3.7 33.7 - - + +
97B VAL 3.6 6.3 - - - +
98B LYS* 3.3 17.8 - - + +
168B PHE* 1.3 71.7 - - - +
170B HIS* 1.3 69.8 + - - +
329B ASN* 6.0 0.2 - - - +
347B TRP* 3.3 25.7 + - + -
350B THR* 4.0 17.9 - - + +
351B LYS* 6.0 0.6 - - - -
354B GLU* 2.5 37.9 + - - +
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Residues in contact with HIS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B THR* 3.3 4.8 - - - -
97B VAL 2.8 41.9 + - - +
164B LYS* 3.4 37.3 - - + +
166B ASP* 2.7 36.9 + - - -
168B PHE* 3.4 26.4 + - + +
169B THR* 1.3 80.4 + - - +
171B LEU* 1.3 60.3 - - - +
172B TYR* 3.7 22.3 - - + -
186B ILE* 4.7 0.9 - - + -
187B ASP* 2.8 28.8 + - - +
347B TRP* 4.4 2.6 + - - -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 3.7 33.2 - - + +
95B PHE 3.7 5.8 - - - +
96B THR* 3.8 20.4 - - + -
170B HIS* 1.3 70.7 - - - +
172B TYR* 1.3 60.5 + - - +
173B THR* 4.1 7.9 - - - +
185B LYS 3.7 0.5 - - - +
186B ILE* 3.2 9.7 - - - +
187B ASP* 2.7 42.3 + - - -
188B ASN* 3.8 32.5 + - + +
329B ASN 5.4 2.0 - - - +
343B GLY* 3.8 26.5 - - - -
346B THR* 4.8 2.7 - - - +
347B TRP* 3.9 20.9 - - + -
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL 3.8 0.3 - - - +
94B GLN* 3.2 5.4 - - - +
95B PHE* 2.9 44.7 + - + +
97B VAL* 4.1 15.7 - - + -
132B PHE* 3.9 16.9 - + + -
134B PRO* 3.7 35.0 - - + +
144B VAL* 4.0 23.3 - - + -
163B CYS* 3.5 5.4 - - - +
164B LYS* 3.0 34.8 + - - +
170B HIS* 3.7 26.2 - - + -
171B LEU* 1.3 71.2 - - - +
173B THR* 1.3 62.3 + - - +
184B VAL* 5.8 0.2 - - + -
185B LYS 3.7 1.8 - - - -
186B ILE* 3.8 37.0 - - + -
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.8 23.3 - - + -
93B VAL 3.4 3.6 - - - +
94B GLN* 2.8 29.2 + - - +
132B PHE* 3.5 8.4 - - - -
171B LEU* 4.1 10.4 - - - +
172B TYR* 1.3 76.5 - - - +
174B LEU* 1.3 62.4 + - - +
175B ILE* 4.1 17.5 - - + -
183B GLU 3.9 0.3 - - - +
184B VAL* 3.4 4.9 - - - -
185B LYS* 2.9 57.9 + - + +
188B ASN* 4.7 2.8 + - - +
339B ALA* 4.8 2.7 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU 3.7 1.2 - - - +
92B VAL* 3.3 6.1 - - - +
93B VAL* 2.8 47.3 + - + +
130B ILE* 4.1 25.6 - - + -
132B PHE* 3.5 31.4 - - + -
146B VAL* 3.9 25.8 - - + -
148B PHE* 5.2 1.1 - - + -
173B THR* 1.3 73.9 - - - +
175B ILE* 1.3 73.3 + - - +
176B VAL* 4.0 22.9 - - + -
182B TYR* 4.6 6.3 - - + -
183B GLU 3.7 8.7 - - - +
184B VAL* 4.0 12.3 - - + -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 4.0 11.0 - - + -
91B LEU 3.5 2.9 - - - +
92B VAL* 4.2 8.3 - - + -
173B THR* 4.1 13.9 - - + -
174B LEU* 1.3 79.7 - - - +
176B VAL* 1.3 64.3 + - - +
177B ARG* 4.0 15.5 - - + +
182B TYR* 3.0 9.4 - - - +
183B GLU* 2.9 50.4 + - + +
185B LYS* 3.8 28.7 - - + -
336B GLU* 3.7 53.4 - - + +
339B ALA* 6.1 0.2 - - + -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 4.8 2.2 - - - +
89B GLN 4.0 1.6 - - - +
90B THR* 3.4 2.9 - - - +
91B LEU* 2.8 52.9 + - + +
130B ILE* 5.1 5.4 - - + -
148B PHE* 3.8 32.8 - - + -
174B LEU* 4.0 21.8 - - + -
175B ILE* 1.3 79.3 - - - +
177B ARG* 1.3 64.2 + - - +
181B THR 3.7 6.1 - - - +
182B TYR* 4.8 2.2 - - + -
196B LEU* 5.0 3.6 - - + -
306B TYR* 3.8 36.7 - - + +
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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
------------------------------------------------------------
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