Contacts of the strand formed by residues 169 - 176 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASP* 5.9 0.6 - - - +
96C THR* 3.6 33.9 - - + +
97C VAL 3.6 5.8 - - - +
98C LYS* 3.3 17.2 - - + +
168C PHE* 1.3 71.7 - - - +
170C HIS* 1.3 68.1 + - - +
329C ASN* 5.9 0.7 - - - +
347C TRP* 3.3 25.6 + - + -
350C THR* 4.0 17.1 - - + +
351C LYS* 6.1 1.1 - - - -
354C GLU* 2.5 38.1 + - - +
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 3.3 5.1 - - - -
97C VAL 2.8 37.2 + - - +
164C LYS* 3.4 39.0 - - + +
166C ASP* 2.7 34.6 + - - -
168C PHE* 3.4 27.0 + - + -
169C THR* 1.3 80.5 + - - +
171C LEU* 1.3 62.0 - - - +
172C TYR* 3.7 22.0 - - + -
186C ILE* 4.7 1.3 - - + -
187C ASP* 2.8 29.0 + - - +
347C TRP* 4.4 2.0 - - - -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLN* 3.7 32.8 - - + +
95C PHE* 3.7 6.1 - - - +
96C THR* 3.8 20.9 - - + -
170C HIS* 1.3 71.2 - - - +
172C TYR* 1.3 59.8 + - - +
173C THR* 4.1 7.6 - - - +
185C LYS 3.7 0.6 - - - +
186C ILE* 3.2 10.4 - - - +
187C ASP* 2.8 39.8 + - - -
188C ASN* 3.8 33.4 - - + +
329C ASN 5.4 1.8 - - - +
343C GLY* 3.7 25.8 - - - -
346C THR* 4.7 2.2 - - - +
347C TRP* 3.9 23.0 - - + -
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Residues in contact with TYR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL 3.8 0.5 - - - +
94C GLN* 3.2 6.5 - - - +
95C PHE* 2.9 42.7 + - + +
97C VAL* 4.1 15.3 - - + -
132C PHE* 3.9 17.3 - + + -
134C PRO* 3.7 35.0 - - + +
144C VAL* 4.0 22.7 - - + -
163C CYS* 3.5 5.7 - - - +
164C LYS* 3.0 35.2 + - - +
170C HIS* 3.7 28.3 - - + -
171C LEU* 1.3 72.0 - - - +
173C THR* 1.3 63.8 + - - +
184C VAL* 5.8 0.2 - - + -
185C LYS 3.6 1.1 - - - -
186C ILE* 3.8 35.9 - - + -
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 3.8 23.1 - - + -
93C VAL 3.4 3.1 - - - +
94C GLN* 2.8 29.3 + - - +
132C PHE* 3.5 8.4 - - - -
171C LEU* 4.1 9.9 - - - +
172C TYR* 1.3 76.1 - - - +
174C LEU* 1.3 61.0 + - - +
175C ILE* 4.0 16.2 - - + -
183C GLU 3.9 0.3 - - - +
184C VAL* 3.4 4.7 - - - -
185C LYS* 2.9 59.4 + - + +
188C ASN* 4.7 2.4 + - - +
339C ALA* 4.9 2.0 - - + -
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU 3.7 1.6 - - - +
92C VAL* 3.3 5.5 - - - +
93C VAL* 2.8 46.4 + - + +
130C ILE* 4.1 26.2 - - + -
132C PHE* 3.4 32.9 - - + -
146C VAL* 3.9 24.2 - - + -
148C PHE* 5.1 0.9 - - + -
173C THR* 1.3 75.0 - - - +
175C ILE* 1.3 70.4 + - - +
176C VAL* 4.0 23.1 - - + -
182C TYR* 4.6 7.2 - - + -
183C GLU 3.7 8.1 - - - +
184C VAL* 4.0 12.3 - - + -
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Residues in contact with ILE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C THR* 4.0 10.8 - - + -
91C LEU 3.5 2.9 - - - +
92C VAL* 4.0 21.1 - - + -
173C THR* 4.0 12.8 - - + -
174C LEU* 1.3 74.9 - - - +
176C VAL* 1.3 63.2 + - - +
177C ARG* 4.0 15.0 - - + +
182C TYR* 3.0 9.0 - - - +
183C GLU* 2.8 58.6 + - + +
185C LYS* 4.9 13.0 - - + +
336C GLU* 3.7 52.5 - - + +
339C ALA* 5.5 0.4 - - + -
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ASN* 4.7 2.5 - - - +
89C GLN 4.0 1.7 - - - +
90C THR* 3.4 3.0 - - - +
91C LEU* 2.8 56.2 + - + +
130C ILE* 5.0 1.3 - - + -
148C PHE* 3.9 29.6 - - + -
174C LEU* 4.0 22.7 - - + -
175C ILE* 1.3 79.1 - - - +
177C ARG* 1.3 64.2 + - - +
181C THR 3.7 6.5 - - - +
182C TYR* 4.7 2.7 - - + -
196C LEU* 4.8 4.3 - - + -
306C TYR* 3.8 37.7 - - + +
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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