Contacts of the strand formed by residues 144 - 150 (chain C) in PDB entry 4LCC
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 144 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C TYR* 3.2 6.5 - - - -
141C VAL* 3.1 35.8 + - + +
142C ASP* 2.5 38.9 + - + +
143C SER* 1.3 80.2 - - - +
145C PRO* 1.3 71.6 - - + +
146C ILE* 3.5 5.4 + - + +
162C TRP* 5.4 5.8 - + + -
288C ALA* 6.2 2.5 - - + -
289C LEU* 4.1 11.9 - - + -
291C ARG* 6.1 1.1 - - - -
319C TYR* 3.0 39.8 + + - -
321C PRO* 4.8 9.0 - - + -
349C GLY* 5.2 2.6 + - - -
351C TYR* 4.1 17.8 + - - -
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Residues in contact with PRO 145 (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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54C SER* 5.9 1.6 - - - +
62C TYR* 5.7 1.6 - - - +
139C GLY 3.7 7.0 - - - +
140C TYR* 3.7 19.7 - - + -
143C SER 3.9 6.1 - - - +
144C HIS* 1.3 87.9 - - + +
146C ILE* 1.3 64.6 + - - +
159C ARG* 3.5 33.2 - - + +
160C ALA* 4.1 4.7 - - - +
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Residues in contact with ILE 146 (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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118C LEU* 4.3 14.6 - - + -
120C TYR* 4.6 2.0 - - - +
139C GLY* 3.1 27.2 + - - +
140C TYR 4.0 1.8 - - - +
141C VAL* 3.5 36.3 - - + +
144C HIS* 3.7 2.5 - - + +
145C PRO* 1.3 79.7 - - - +
147C THR* 1.3 78.5 + - + +
158C PRO* 3.3 6.4 - - - +
159C ARG* 2.4 32.6 + - - +
160C ALA* 3.9 4.2 + - + +
162C TRP* 4.0 12.3 - - + -
163C MET* 3.6 36.5 - - + +
281C PHE* 4.4 7.2 - - + -
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Residues in contact with THR 147 (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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120C TYR* 3.8 15.1 - - + +
137C SER* 4.8 2.3 + - - -
138C ALA* 3.1 11.2 - - - +
139C GLY* 2.8 37.4 + - - +
145C PRO* 5.8 0.3 - - - +
146C ILE* 1.3 95.4 + - + +
148C MET* 1.3 62.3 + - - +
156C LYS* 3.4 36.6 - - - +
157C GLU 3.8 4.0 - - - -
159C ARG* 4.7 1.1 - - - +
163C MET* 5.7 3.1 - - + -
171C HIS* 6.4 0.4 - - + -
172C TRP* 4.3 13.2 - - + -
281C PHE* 6.0 2.5 - - + -
401C 1XL 4.5 1.2 + - - -
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Residues in contact with MET 148 (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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52C ASP* 3.8 27.1 - - + +
53C LEU* 4.0 14.8 - - + +
136C ILE* 3.8 28.3 - - + -
137C SER 3.4 6.3 - - - +
138C ALA* 4.2 9.6 - - + -
147C THR* 1.3 77.8 - - - +
149C TYR* 1.3 73.6 + - - +
150C ASN* 4.8 12.3 + - + +
155C LEU 3.3 5.2 - - - +
156C LYS* 3.5 3.5 - - - +
157C GLU* 3.1 31.7 + - - +
159C ARG* 3.3 44.2 - - + +
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Residues in contact with TYR 149 (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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135C PHE* 3.5 37.0 - + - -
136C ILE* 3.4 2.9 - - - +
137C SER* 2.6 50.1 + - - +
148C MET* 1.3 77.5 - - - +
150C ASN* 1.3 68.2 + - - +
154C GLN* 3.2 22.3 - - + +
155C LEU* 3.0 41.7 - - - +
156C LYS* 4.4 6.7 - - + -
175C TYR 5.0 0.2 - - - -
176C THR* 4.3 10.3 - - - -
179C LEU* 3.6 34.8 - - + -
180C ARG* 3.3 14.2 - - - +
183C GLN* 2.8 21.9 + - - -
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Residues in contact with ASN 150 (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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133C PRO* 4.1 17.5 - - + -
135C PHE 3.4 7.4 - - - +
136C ILE* 4.5 5.4 - - + +
148C MET* 4.9 12.7 + - - +
149C TYR* 1.3 85.4 - - - +
151C SER* 1.3 59.7 + - - +
152C VAL* 3.6 8.0 + - - +
153C SER* 3.1 56.8 + - - +
154C GLN* 3.4 10.0 - - - -
155C LEU 4.3 2.0 + - - -
159C ARG* 6.1 0.8 - - - +
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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