Contacts of the helix formed by residues 112 - 125 (chain L) in PDB entry 3CX5
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 SER 112 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89L GLU 5.2 4.0 + - - -
90L GLY 5.7 0.9 - - - -
91L LEU* 4.9 3.6 - - - -
108L SER* 3.3 21.7 + - - -
109L LEU* 3.0 21.0 + - - +
111L GLY* 1.3 78.3 - - - +
113L THR* 1.3 63.2 + - - +
114L ASP* 3.1 3.8 - - - +
115L LYS* 3.1 24.4 + - - +
116L SER* 3.4 7.3 + - - -
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Residues in contact with THR 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L ALA* 5.3 2.7 - - - -
51L VAL* 3.8 18.5 - - - +
108L SER* 3.9 7.5 + - - -
109L LEU 3.9 0.9 + - - -
110L PRO 3.7 17.8 + - - +
111L GLY 3.5 1.3 - - - -
112L SER* 1.3 78.1 - - - +
114L ASP* 1.3 77.0 + - - +
116L SER* 3.3 14.9 + - - -
117L LEU* 3.3 17.5 + - + +
214L ILE* 4.1 19.6 - - + +
218L ASP* 5.6 11.7 - - + +
219L LEU* 4.5 11.7 - - - +
222L SER* 5.9 1.3 - - - +
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Residues in contact with ASP 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L GLY 3.7 17.3 - - - +
112L SER* 3.1 0.8 - - - -
113L THR* 1.3 88.0 - - - +
115L LYS* 1.3 63.6 + - + +
116L SER 3.3 0.2 + - - -
117L LEU* 3.3 10.8 + - - +
118L ASP* 3.2 32.0 + - - +
222L SER* 3.8 19.3 + - - +
226L LYS* 5.2 0.9 + - - +
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Residues in contact with LYS 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L GLU* 3.2 49.3 + - + +
91L LEU* 3.6 20.5 - - + +
112L SER* 3.1 18.2 + - - +
114L ASP* 1.3 79.7 - - + +
116L SER* 1.3 61.0 + - - +
118L ASP* 3.6 19.1 + - - +
119L PHE* 3.3 16.1 + - - +
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Residues in contact with SER 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L VAL* 4.2 22.0 - - - +
91L LEU* 4.0 9.4 - - - +
106L VAL* 4.0 24.0 + - - +
108L SER* 3.1 30.8 + - - -
112L SER 3.4 1.6 + - - -
113L THR* 3.3 10.9 + - - -
114L ASP 3.2 0.2 - - - -
115L LYS* 1.3 77.2 - - - +
117L LEU* 1.3 60.1 + - - +
119L PHE* 3.2 4.9 + - - +
120L LEU* 2.9 29.1 + - - +
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L VAL* 3.6 23.6 - - + -
113L THR* 3.3 13.0 + - - +
114L ASP* 3.3 10.1 + - - +
116L SER* 1.3 76.9 - - - +
118L ASP* 1.3 60.0 + - - +
120L LEU* 3.6 9.7 - - + +
121L ASN* 2.8 31.5 + - - +
208L VAL* 4.8 4.0 - - + -
219L LEU* 3.5 28.0 - - + -
222L SER* 3.5 31.2 - - - -
223L ILE* 4.0 21.8 - - + -
226L LYS* 4.3 11.2 + - - +
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Residues in contact with ASP 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L ASP* 3.2 23.8 + - - +
115L LYS* 3.8 23.4 - - + +
116L SER 3.3 0.2 - - - -
117L LEU* 1.3 75.8 - - - +
119L PHE* 1.3 60.9 + - - +
121L ASN* 3.6 7.1 + - - +
122L GLN* 3.3 21.3 + - - +
126L GLN* 5.1 0.5 - - - +
226L LYS* 3.5 24.9 + - - -
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Residues in contact with PHE 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 4.3 5.6 - + - -
82L ASN* 3.4 51.4 - - - -
85L VAL* 4.0 17.9 - - + -
86L ALA* 3.6 26.7 - - + -
89L GLU* 6.4 0.4 - - + -
91L LEU* 4.0 11.4 - - + -
93L LEU* 3.6 19.5 - - + -
106L VAL* 4.1 15.0 - - + -
115L LYS 3.3 11.2 + - - +
116L SER* 3.2 8.6 + - - +
117L LEU 3.2 0.2 - - - -
118L ASP* 1.3 77.3 - - - +
120L LEU* 1.3 62.1 + - - +
122L GLN* 3.2 15.0 + - - +
123L SER* 3.0 46.6 + - - -
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Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L VAL* 4.5 5.6 - - + +
52L GLY* 4.3 13.0 - - - +
53L VAL* 3.9 18.8 - - + +
77L PHE* 4.8 6.7 - - + -
104L TYR 4.1 16.2 - - - +
106L VAL* 3.6 26.7 - - + -
116L SER 2.9 14.9 + - - +
117L LEU* 3.6 13.9 - - + +
119L PHE* 1.3 78.8 - - + +
121L ASN* 1.3 61.6 + - - +
123L SER* 3.3 2.8 + - - -
124L PHE* 3.2 47.4 + - + +
125L ILE* 5.5 0.2 - - - +
208L VAL* 6.2 2.5 - - + -
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Residues in contact with ASN 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L LEU 2.8 17.5 + - - +
118L ASP* 3.7 9.0 - - - +
119L PHE 3.2 0.2 - - - -
120L LEU* 1.3 77.2 - - - +
122L GLN* 1.3 51.5 + - - +
125L ILE* 3.0 27.1 + - - +
126L GLN* 2.8 45.7 + - - +
226L LYS* 4.4 19.8 - - - +
228L LEU* 3.3 31.3 - - - +
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Residues in contact with GLN 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82L ASN* 5.2 3.6 - - - +
85L VAL* 4.2 20.9 - - - +
118L ASP 3.3 10.6 + - - +
119L PHE* 3.2 20.4 + - - +
121L ASN* 1.3 80.7 - - - +
123L SER* 1.3 57.4 + - - +
126L GLN* 3.3 27.5 + - - +
127L GLN* 3.1 56.9 + - - +
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Residues in contact with SER 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 4.2 16.6 - - - -
82L ASN* 3.8 13.5 + - - -
119L PHE* 3.0 37.2 + - - -
120L LEU* 3.8 6.3 - - - -
121L ASN 3.3 0.2 - - - -
122L GLN* 1.3 80.8 + - - +
124L PHE* 1.3 67.8 + - - +
127L GLN 3.1 9.5 - - - +
128L LYS* 3.5 18.9 + - - +
131L LEU* 4.8 14.0 - - - +
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Residues in contact with PHE 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53L VAL* 3.6 17.0 - - + -
55L PHE* 3.7 28.3 - + + -
77L PHE* 4.5 13.9 - + - -
104L TYR* 3.6 40.6 - + + -
120L LEU* 3.2 31.6 + - + +
122L GLN 3.5 0.2 - - - -
123L SER* 1.3 81.8 - - - +
125L ILE* 1.3 71.3 + - + +
127L GLN 3.6 8.0 - - - +
128L LYS* 3.4 42.3 - - - +
201L PHE* 4.0 13.5 - + + -
231L GLN* 4.5 9.8 + - - -
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Residues in contact with ILE 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ASN* 3.0 27.7 + - - +
124L PHE* 1.3 85.0 - - + +
126L GLN* 1.3 69.2 + - - +
127L GLN* 3.4 1.9 + - - -
128L LYS* 5.5 0.7 - - - +
228L LEU* 3.6 48.5 - - + -
231L GLN* 4.1 28.1 - - + +
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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