Contacts of the helix formed by residues 89 - 105 (chain C) in PDB entry 4LSZ
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 GLY 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LYS* 5.4 2.8 - - - +
88C ASN* 1.3 73.9 + - - +
90C THR* 1.3 62.5 + - - +
91C ASP* 3.3 4.1 - - - +
92C LYS* 3.4 12.4 + - - +
93C ASP* 3.3 14.4 + - - -
233D ARG* 4.9 0.9 - - - -
234D SER 4.0 7.9 - - - -
235D PRO 3.2 15.7 + - - -
236D GLY 5.0 1.6 - - - -
237D ARG 5.0 0.2 - - - -
238D GLY* 3.4 20.4 - - - -
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Residues in contact with THR 90 (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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74C ASN* 2.7 29.0 + - - +
76C LYS* 3.5 28.0 - - + -
87C ARG* 2.9 57.9 + - - +
88C ASN 3.3 1.0 + - - -
89C GLY* 1.3 76.3 - - - +
91C ASP* 1.3 64.7 + - - +
93C ASP* 3.1 11.0 + - - +
94C ALA 2.9 24.6 + - - -
142C LEU* 3.8 9.0 - - - +
233D ARG* 4.6 1.9 - - - +
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASN* 3.1 23.5 + - - +
76C LYS* 3.4 38.0 + - - +
89C GLY* 3.3 2.1 - - - +
90C THR* 1.3 77.7 - - - +
92C LYS* 1.3 58.5 + - + +
94C ALA* 3.3 3.3 + - - +
95C GLU* 2.9 35.7 + - + +
112C ASN* 4.9 0.9 - - - +
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Residues in contact with LYS 92 (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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89C GLY* 3.4 15.2 + - - +
90C THR 3.3 0.2 - - - -
91C ASP* 1.3 74.5 - - + +
93C ASP* 1.3 66.8 + - - +
95C GLU* 4.1 4.8 - - - +
96C ALA* 2.9 27.7 + - - +
236D GLY* 3.2 28.7 + - - +
237D ARG* 4.4 15.5 - - - +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 4.9 2.6 + - - -
89C GLY 3.3 7.3 + - - +
90C THR* 3.1 17.2 + - - +
92C LYS* 1.3 79.7 - - - +
94C ALA* 1.3 58.7 + - - +
96C ALA* 3.8 0.8 - - - -
97C LEU* 2.9 35.9 + - - +
142C LEU* 4.2 11.5 - - + +
184C GLN* 4.7 2.9 - - - +
233D ARG* 5.0 0.9 - - - -
237D ARG 4.3 2.1 - - - +
238D GLY* 3.4 6.9 - - - -
239D SER* 2.9 45.6 + - - +
242D VAL* 3.4 30.1 - - + +
243D GLN* 4.5 2.1 + - - +
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Residues in contact with ALA 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 4.3 7.5 - - + +
74C ASN* 3.8 30.5 - - + +
90C THR 2.9 15.4 + - - +
91C ASP* 3.8 4.3 - - - +
93C ASP* 1.3 76.8 - - - +
95C GLU* 1.3 61.4 + - + +
97C LEU* 3.9 4.6 - - - +
98C PHE* 2.9 29.1 + - - +
110C VAL* 4.4 15.7 - - + +
142C LEU* 4.1 9.4 - - + -
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Residues in contact with GLU 95 (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 ASP* 2.9 20.3 + - + +
92C LYS* 4.1 5.8 - - - +
94C ALA* 1.3 79.0 - - + +
96C ALA* 1.3 64.7 + - - +
98C PHE* 3.3 21.9 + - - +
99C LYS* 3.1 38.8 + - - +
110C VAL* 5.5 5.7 - - - +
23F ARG* 6.2 0.5 - - - -
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Residues in contact with ALA 96 (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 LYS 2.9 19.0 + - - +
93C ASP* 3.9 3.1 - - - +
95C GLU* 1.3 75.8 - - - +
97C LEU* 1.3 58.4 + - - +
99C LYS* 3.2 9.1 + - - +
100C CYS* 2.9 31.6 + - - +
242D VAL* 5.2 0.9 - - + -
246D CYS* 3.6 20.6 - - + -
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Residues in contact with LEU 97 (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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72C ILE* 4.0 13.7 - - + -
93C ASP 2.9 21.2 + - - +
94C ALA* 3.9 4.0 - - - +
96C ALA* 1.3 72.6 - - - +
98C PHE* 1.3 67.4 + - - +
100C CYS 4.5 0.2 - - - +
101C PHE* 3.0 54.4 + - + +
140C ILE* 3.7 31.6 - - + -
142C LEU* 4.0 20.4 - - + -
242D VAL* 3.6 20.2 - - + -
245D LEU* 3.9 17.9 - - + -
246D CYS* 3.7 16.8 - - - -
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ILE* 4.1 0.8 - - - +
94C ALA 2.9 19.8 + - - +
95C GLU* 3.3 22.0 + - - +
97C LEU* 1.3 77.1 - - - +
99C LYS* 1.3 72.1 + - + +
102C ARG* 3.1 61.3 + - + +
108C VAL* 3.8 49.6 - - + +
109C ILE* 5.3 1.1 - - - -
110C VAL* 4.2 17.7 - - + -
20F GLU* 5.0 1.8 - - - -
23F ARG* 3.6 44.2 - - - -
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Residues in contact with LYS 99 (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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95C GLU* 3.1 28.2 + - - +
96C ALA* 3.7 9.9 - - - +
97C LEU 3.2 0.2 - - - -
98C PHE* 1.3 86.1 - - + +
100C CYS* 1.3 60.1 + - - +
102C ARG* 3.4 21.3 + - - +
103C SER* 2.9 30.4 + - - -
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Residues in contact with CYS 100 (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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96C ALA* 2.9 14.0 + - - +
97C LEU 4.0 2.7 - - - +
99C LYS* 1.3 76.5 - - - +
101C PHE* 1.3 73.2 + - + +
103C SER* 3.1 9.5 + - - -
104C LEU* 3.0 25.6 + - - +
246D CYS* 3.4 49.8 - - - -
249D LEU* 4.3 16.9 - - + +
250D GLU* 4.4 11.2 - - - -
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Residues in contact with PHE 101 (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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70C CYS* 4.0 16.8 - - - -
97C LEU* 3.0 35.1 + - + +
100C CYS* 1.3 81.7 - - + +
102C ARG* 1.3 59.7 + - - +
104C LEU* 3.3 11.2 + - + -
105C GLY 3.3 5.2 + - - -
106C PHE* 3.1 55.1 + + + +
108C VAL* 4.0 15.9 - - + -
138C ALA* 4.4 4.9 - - + -
140C ILE* 3.7 21.8 - - + -
180C LEU* 5.8 0.2 - - + -
182C PHE* 3.8 40.8 - + - -
245D LEU* 4.3 2.5 - - + -
249D LEU* 3.6 29.2 - - + -
301D PHE* 5.7 2.2 - + - -
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Residues in contact with ARG 102 (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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98C PHE* 3.1 48.8 + - + +
99C LYS* 3.6 21.9 + - - +
101C PHE* 1.3 76.7 - - - +
103C SER* 1.3 61.8 + - - +
105C GLY* 3.1 15.1 + - - -
106C PHE 3.7 16.2 - - - +
107C ASP* 6.0 0.2 - - - -
108C VAL* 3.8 8.1 - - + +
20F GLU* 3.2 38.0 + - - +
23F ARG* 5.6 0.9 - - - +
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Residues in contact with SER 103 (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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99C LYS 2.9 14.8 + - - -
100C CYS* 3.3 12.6 - - - -
102C ARG* 1.3 78.0 - - - +
104C LEU* 1.3 62.1 + - - +
105C GLY* 3.4 0.7 + - - -
254D LYS* 3.1 33.6 + - - -
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Residues in contact with LEU 104 (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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67C LEU* 3.3 21.8 - - + +
100C CYS 3.0 17.2 + - - +
101C PHE* 3.5 15.9 - - + +
102C ARG 3.3 0.4 - - - -
103C SER* 1.3 78.0 - - - +
105C GLY* 1.3 57.0 + - - +
106C PHE* 4.1 13.5 - - + -
249D LEU* 4.2 28.3 - - + +
253D GLY* 3.7 38.4 - - - +
254D LYS* 4.3 14.7 - - + +
301D PHE* 4.0 36.9 - - + +
303D GLN* 5.7 4.0 - - - +
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Residues in contact with GLY 105 (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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66C LYS* 5.5 3.5 - - - +
67C LEU* 3.6 22.3 + - - +
68C GLY 4.6 0.7 + - - +
102C ARG 3.1 12.2 + - - -
103C SER 3.2 0.9 - - - -
104C LEU* 1.3 79.4 - - - +
106C PHE* 1.3 67.3 + - - +
107C ASP* 3.7 5.9 + - - +
303D GLN* 6.3 1.6 - - - -
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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