Contacts of the strand formed by residues 169 - 176 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F ASP* 5.9 0.6 - - - +
96F THR* 3.6 32.1 - - + +
97F VAL 3.6 5.4 - - - +
98F LYS* 3.3 17.8 - - + +
168F PHE* 1.3 71.7 - - - +
170F HIS* 1.3 73.0 + - - +
329F ASN* 5.9 1.1 - - - +
347F TRP* 3.3 22.2 + - + -
350F THR* 4.0 17.5 - - + +
351F LYS* 6.0 0.6 - - - -
354F GLU* 2.5 38.4 + - - +
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Residues in contact with HIS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F THR* 3.3 5.0 - - - -
97F VAL 2.8 37.8 + - - +
164F LYS* 3.3 37.0 - - + +
166F ASP* 2.6 40.7 + - - -
168F PHE* 3.4 22.2 + - - +
169F THR* 1.3 81.0 + - - +
171F LEU* 1.3 60.5 - - - +
172F TYR* 3.7 22.0 - - + -
186F ILE* 4.7 1.3 - - + -
187F ASP* 2.9 30.2 + - - +
347F TRP* 4.4 2.9 - - - -
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F GLN* 3.6 33.2 - - + +
95F PHE 3.7 6.1 - - - +
96F THR* 3.8 20.6 - - + -
170F HIS* 1.3 70.9 - - - +
172F TYR* 1.3 60.1 + - - +
173F THR* 4.1 7.2 - - - +
185F LYS 3.7 0.5 - - - +
186F ILE* 3.2 10.4 - - - +
187F ASP* 2.7 39.6 + - - -
188F ASN* 3.8 32.8 - - + +
329F ASN 5.4 2.0 - - - +
343F GLY* 3.7 26.2 - - - -
346F THR* 4.8 2.0 - - - +
347F TRP* 3.9 24.2 - - + -
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Residues in contact with TYR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F VAL 3.8 0.7 - - - +
94F GLN* 3.2 6.4 - - - +
95F PHE* 2.9 42.8 + - + +
97F VAL* 4.1 15.0 - - + -
132F PHE* 3.9 16.9 - + + -
134F PRO* 3.7 35.9 - - + +
144F VAL* 4.0 23.8 - - + -
163F CYS* 3.5 5.2 - - - +
164F LYS* 3.0 35.3 + - - +
170F HIS* 3.7 27.8 - - + -
171F LEU* 1.3 71.2 - - - +
173F THR* 1.3 61.8 + - - +
184F VAL* 5.8 0.2 - - + -
185F LYS 3.6 2.5 - - - -
186F ILE* 3.8 35.4 - - + -
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Residues in contact with THR 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F VAL* 3.8 22.7 - - + -
93F VAL 3.4 3.1 - - - +
94F GLN* 2.8 29.6 + - - +
132F PHE* 3.5 8.6 - - - -
171F LEU* 4.1 10.2 - - - +
172F TYR* 1.3 76.6 - - - +
174F LEU* 1.3 61.9 + - - +
175F ILE* 4.1 17.7 - - + -
183F GLU 3.9 0.5 - - - +
184F VAL* 3.4 4.7 - - - -
185F LYS* 2.9 56.9 + - + +
188F ASN* 4.7 2.8 + - - +
339F ALA* 4.9 2.5 - - + -
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Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 3.7 1.1 - - + +
92F VAL* 3.3 6.6 - - - +
93F VAL* 2.8 46.8 + - + +
130F ILE* 4.1 26.5 - - + -
132F PHE* 3.5 31.3 - - + -
146F VAL* 3.9 24.9 - - + -
148F PHE* 5.2 1.1 - - + -
173F THR* 1.3 74.3 - - - +
175F ILE* 1.3 72.7 + - - +
176F VAL* 4.0 22.7 - - + -
182F TYR* 4.7 6.1 - - + -
183F GLU 3.7 9.2 - - - +
184F VAL* 4.0 12.8 - - + -
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Residues in contact with ILE 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F THR* 4.0 10.5 - - + -
91F LEU 3.5 2.7 - - - +
92F VAL* 4.2 7.9 - - + -
173F THR* 4.1 13.2 - - + -
174F LEU* 1.3 76.0 - - - +
176F VAL* 1.3 64.0 + - - +
177F ARG* 4.0 15.7 - - + +
182F TYR* 3.0 8.8 - - - +
183F GLU* 2.8 53.1 + - + +
185F LYS* 4.2 29.8 - - + +
336F GLU* 3.7 54.1 - - + +
339F ALA* 6.1 0.2 - - + -
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ASN* 4.7 2.5 - - - +
89F GLN 4.0 1.6 - - - +
90F THR* 3.4 2.9 - - - +
91F LEU* 2.8 56.1 + - + +
130F ILE* 5.1 1.6 - - + -
148F PHE* 3.9 29.6 - - + -
174F LEU* 4.0 21.8 - - + -
175F ILE* 1.3 80.0 - - - +
177F ARG* 1.3 64.6 + - - +
181F THR 3.8 5.8 - - - +
182F TYR* 4.8 3.1 - - + -
196F LEU* 5.0 3.6 - - + -
306F TYR* 3.8 38.8 - - + +
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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