Contacts of the strand formed by residues 116 - 125 (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 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ARG* 3.7 12.0 + - - -
115C THR* 1.3 75.6 - - - +
117C SER* 1.3 57.4 + - - +
142C ASP* 3.1 28.0 - - - +
212C GLU* 3.5 1.4 - - - +
213C LEU* 2.8 41.6 + - + +
214C LEU 6.1 0.2 - - - -
215C GLU* 6.0 3.1 - - - -
278C LEU* 4.3 7.0 - - + -
282C LEU* 4.0 35.7 - - + +
289C LEU* 5.3 5.2 - - + +
290C GLN* 5.9 5.3 + - - +
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Residues in contact with SER 117 (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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115C THR* 4.3 4.3 + - - -
116C HIS* 1.3 78.1 - - - +
118C LEU* 1.3 61.1 + - - +
119C ARG* 3.4 23.4 + - - +
140C TYR 4.0 0.6 + - - +
141C VAL* 3.3 10.0 - - - +
142C ASP* 2.9 39.1 + - - -
143C SER 5.2 0.9 + - - -
211C CYS 3.6 5.6 - - - -
212C GLU* 3.3 27.4 - - - +
222C PHE* 5.6 0.4 - - - -
278C LEU* 3.7 7.8 - - - +
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Residues in contact with LEU 118 (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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117C SER* 1.3 73.8 - - - +
119C ARG* 1.3 72.2 + - - +
120C TYR* 3.8 31.2 - - + -
140C TYR 3.5 9.0 - - - +
141C VAL* 4.2 9.9 - - + -
146C ILE* 4.3 7.6 - - + -
210C GLY* 3.1 21.8 - - - -
211C CYS* 2.8 19.3 + - - +
222C PHE* 3.8 0.5 - - - -
269C TRP* 5.2 1.1 - - + -
274C CYS* 3.9 22.4 - - - +
277C TRP* 4.1 23.3 - - + -
278C LEU* 3.7 18.8 - - + +
281C PHE* 4.1 24.5 - - + -
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Residues in contact with ARG 119 (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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57C LYS* 4.4 33.6 - - - +
117C SER* 3.4 27.1 + - - +
118C LEU* 1.3 82.2 - - - +
120C TYR* 1.3 65.1 + - - +
121C PHE* 3.8 29.8 - - + -
138C ALA 4.1 0.2 - - - +
139C GLY* 3.4 2.4 - - - -
140C TYR* 2.7 49.7 + - + +
143C SER* 5.8 1.8 + - - -
208C MET* 4.2 9.0 - - + +
209C ILE 3.6 4.3 - - - +
212C GLU* 4.3 11.9 + - - -
222C PHE* 3.5 35.9 - - + -
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Residues in contact with TYR 120 (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* 3.8 30.3 - - + -
119C ARG* 1.3 76.2 - - - +
121C PHE* 1.3 61.4 + - - +
137C SER* 5.5 0.4 - - - -
138C ALA 3.8 2.7 - - - -
139C GLY* 3.5 26.9 - - - -
146C ILE* 4.6 3.2 - - + +
147C THR* 3.8 14.2 - - + +
156C LYS* 5.2 0.7 + - - -
207C ARG* 3.5 1.7 + - - +
208C MET* 3.4 6.8 - - - +
209C ILE* 2.8 47.0 + - + +
210C GLY* 5.6 0.7 - - - -
269C TRP* 4.4 16.2 - + - -
277C TRP* 5.7 2.8 - + + +
281C PHE* 3.7 26.0 - - - -
401C 1XL 3.7 66.6 + + + -
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Residues in contact with PHE 121 (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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55C PHE* 3.5 42.0 - + + -
56C SER 3.4 33.0 - - - -
57C LYS* 4.4 1.1 - - + -
59C TRP* 5.0 9.2 - + - -
119C ARG* 3.8 29.6 - - + -
120C TYR* 1.3 77.6 - - - +
122C ARG* 1.3 63.2 + - - +
136C ILE 3.7 0.6 - - - +
137C SER* 3.3 7.6 - - - -
138C ALA 3.0 28.5 + - - +
140C TYR* 3.6 27.8 - + + -
206C GLN* 6.0 2.7 - - + -
207C ARG 3.3 11.7 - - - -
208C MET* 3.7 33.4 - - + -
401C 1XL 3.7 4.8 + - - -
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Residues in contact with ARG 122 (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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55C PHE* 5.2 0.7 - - - -
121C PHE* 1.3 74.4 - - - +
123C LEU* 1.3 61.5 + - - +
124C GLY 4.1 0.7 - - - -
135C PHE* 4.2 16.1 - - + -
136C ILE 3.4 3.4 - - - -
182C TRP* 3.3 40.2 + - - +
185C MET* 4.9 12.1 - - - +
186C PHE* 3.5 36.5 - - + -
206C GLN* 3.1 11.3 - - - +
207C ARG* 2.9 63.4 + - + +
225C TYR* 4.7 2.8 + - - -
401C 1XL 3.1 66.5 + - - +
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Residues in contact with LEU 123 (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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33C PRO* 4.8 7.2 - - + -
53C LEU* 5.0 2.2 - - + -
55C PHE* 3.5 30.1 - - + -
61C PHE* 3.7 21.3 - - + -
122C ARG* 1.3 74.5 - - - +
124C GLY* 1.3 63.9 + - - +
125C ILE* 3.5 28.3 - - + -
132C ILE 6.3 0.7 - - - +
133C PRO 4.7 2.0 - - - +
134C GLU 3.3 1.7 - - - +
135C PHE* 3.1 9.1 - - - -
136C ILE* 2.7 56.7 + - + +
186C PHE* 4.2 1.6 - - - -
204C THR* 4.7 7.6 - - - -
205C TYR 4.1 0.2 - - - +
206C GLN* 3.5 26.2 - - + -
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Residues in contact with GLY 124 (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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123C LEU* 1.3 74.5 - - - +
125C ILE* 1.3 72.9 + - - +
134C GLU* 3.1 7.2 - - - -
135C PHE* 4.6 2.2 - - - -
186C PHE* 3.5 19.2 - - - -
190C LEU* 4.0 11.4 - - - -
204C THR* 3.6 0.9 - - - -
205C TYR 2.7 34.0 + - - +
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Residues in contact with ILE 125 (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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33C PRO* 4.5 10.8 - - + -
34C GLN* 4.5 9.0 - - - +
123C LEU* 3.5 23.6 - - + -
124C GLY* 1.3 82.3 - - - +
126C SER* 1.3 63.3 + - - +
127C GLU* 3.1 38.8 - - + +
132C ILE 4.8 2.0 - - - +
133C PRO 3.9 9.9 - - - +
134C GLU* 2.5 50.9 + - - +
190C LEU* 3.8 6.5 - - - +
202C PHE* 5.2 1.8 - - + -
203C HIS 3.9 5.6 - - - +
204C THR* 3.8 25.8 - - + -
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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