Contacts of the strand formed by residues 118 - 128 (chain C) in PDB entry 1HCJ
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 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C PRO* 3.4 24.9 + - + +
14C ILE 4.1 0.7 - - - -
15C LEU* 3.8 24.0 + - + +
114C PHE* 3.4 4.7 - - - -
115C GLU 2.9 38.7 + - - +
116C GLY 3.4 0.2 - - - -
117C ASP* 1.3 101.6 - - - +
119C LEU* 1.3 67.8 + - - +
120C VAL* 3.5 6.1 + - - +
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Residues in contact with LEU 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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8C PHE* 4.2 2.5 - - + -
12C VAL* 3.9 7.1 - - + +
13C PRO 2.8 12.2 + - - +
14C ILE* 3.2 7.1 - - + +
15C LEU 2.9 23.9 + - - +
68C VAL* 3.8 21.5 - - + -
70C CYS* 3.8 24.7 - - - -
71C PHE* 3.3 37.2 - - + -
88C MET* 3.9 17.7 - - + -
112C VAL* 3.9 8.3 - - + -
113C LYS 3.8 5.8 - - - -
114C PHE* 3.8 28.0 - - + -
117C ASP 4.0 1.0 + - - -
118C THR* 1.3 69.6 - - - +
120C VAL* 1.3 58.2 + - - +
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Residues in contact with VAL 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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15C LEU* 3.2 23.8 - - + +
111C GLU 3.4 1.8 - - - +
112C VAL* 3.4 4.9 - - - +
113C LYS* 2.9 43.9 + - + +
115C GLU* 2.8 49.1 - - + +
118C THR* 3.6 18.6 - - + +
119C LEU* 1.3 76.4 - - - +
121C ASN* 1.3 58.2 - - - +
122C ARG* 4.4 15.5 - - + +
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Residues in contact with ASN 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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15C LEU 2.9 11.3 + - - +
16C VAL* 3.3 8.8 - - + +
17C GLU 2.8 32.1 + - - +
63C THR 3.2 13.7 + - - +
64C PHE 3.0 23.4 - - - +
66C GYS 3.7 7.4 + - - -
68C VAL* 3.6 24.0 - - + -
110C ALA* 3.4 26.7 - - - +
111C GLU 3.5 2.2 - - - -
112C VAL* 3.7 12.5 - - + +
120C VAL* 1.3 71.4 - - - +
122C ARG* 1.3 56.8 + - - +
123C ILE* 3.4 9.8 - - - +
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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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15C LEU* 6.2 2.2 - - - +
17C GLU* 3.4 32.3 - - + +
109C ARG 4.0 0.5 - - - +
110C ALA* 3.2 2.4 - - - -
111C GLU* 3.0 40.0 + - + +
113C LYS* 5.3 6.7 - - - +
115C GLU* 2.6 42.8 + - - +
120C VAL* 4.7 12.4 - - + +
121C ASN* 1.3 74.4 - - - +
123C ILE* 1.3 61.5 - - - +
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Residues in contact with ILE 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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16C VAL* 3.8 15.5 - - + -
17C GLU 2.8 19.7 + - - +
18C LEU* 3.2 26.0 - - + +
19C ASP* 3.0 23.9 + - - +
63C THR* 3.6 35.4 - - + +
64C PHE* 4.3 2.2 - - + -
108C THR* 4.4 7.4 - - - -
109C ARG 3.5 7.2 - - - +
110C ALA* 3.7 8.1 - - + -
121C ASN* 3.4 34.8 - - - +
122C ARG* 1.3 80.3 - - - +
124C GLU* 1.3 77.1 + - - +
125C LEU 4.3 0.4 - - - +
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Residues in contact with GLU 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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19C ASP* 3.5 14.4 - - + +
107C LYS 4.0 0.7 - - - +
108C THR* 3.4 2.9 - - - -
109C ARG* 2.9 40.8 + - + +
123C ILE* 1.3 80.6 - - - +
125C LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 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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18C LEU* 3.7 18.4 - - + -
19C ASP 3.1 7.8 + - - +
20C GLY* 3.3 3.8 - - - -
21C ASP* 3.0 29.6 + - - +
22C VAL* 3.8 22.0 - - + -
27C PHE* 4.5 6.5 - - + -
60C LEU* 3.7 29.4 - - + -
63C THR* 4.4 9.0 - - + +
106C TYR* 4.0 19.1 - - + -
107C LYS 3.4 5.2 - - - +
108C THR* 3.9 22.4 - - + -
124C GLU* 1.3 74.9 - - - +
126C LYS* 1.3 74.7 + - - +
127C GLY 3.8 4.0 - - - +
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Residues in contact with LYS 126 (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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21C ASP* 3.3 18.6 - - + +
107C LYS* 2.7 60.7 + - + +
125C LEU* 1.3 79.0 - - - +
127C GLY* 1.3 62.0 - - - +
128C ILE* 3.4 29.6 - - + -
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Residues in contact with GLY 127 (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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21C ASP 2.8 9.1 + - - -
22C VAL* 3.4 6.5 - - - -
23C ASN 2.9 26.3 + - - -
105C ASN 3.0 11.9 - - - -
106C TYR* 3.9 9.0 - - - -
125C LEU* 3.8 2.8 - - - +
126C LYS* 1.3 76.1 - - - +
128C ILE* 1.3 64.1 + - - +
130C PHE* 3.9 12.8 - - - -
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Residues in contact with ILE 128 (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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23C ASN* 3.5 5.8 - - - +
104C GLY* 3.1 4.2 - - - -
105C ASN* 2.9 53.5 + - - +
107C LYS* 2.9 17.7 - - + +
126C LYS* 3.4 26.5 - - + -
127C GLY* 1.3 71.3 - - - +
129C ASP* 1.3 94.5 + - - +
130C PHE* 3.3 3.4 - - - -
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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