Contacts of the helix formed by residues 119 - 133 (chain C) in PDB entry 4MDK
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 ASN 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C GLU* 3.1 18.5 + - - +
68C TYR* 3.7 9.0 - - - -
114C TRP* 4.8 0.2 - - - -
117C THR 4.9 5.0 + - - +
118C GLN* 1.3 75.3 - - - +
120C VAL* 1.3 63.1 + - - +
121C ARG* 3.3 13.7 + - - +
122C THR* 2.5 54.7 + - - +
123C ILE* 3.1 16.4 + - - +
11F LYS* 5.5 7.3 - - - +
8G LEU 5.8 1.4 + - - -
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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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13C LEU* 5.5 0.2 - - + -
16C GLU* 2.8 28.7 + - - +
20C LEU* 3.8 15.3 - - + -
41C TRP* 3.8 26.7 - - + -
62C LEU* 3.9 19.5 - - + -
64C PHE* 3.7 32.3 - - + -
68C TYR* 3.8 3.3 + - + +
119C ASN* 1.3 72.0 - - - +
121C ARG* 1.3 57.2 + - - +
123C ILE* 3.1 12.2 + - + +
124C LEU* 2.9 39.1 + - + +
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLU* 4.3 1.4 + - - -
19C GLY* 3.2 24.0 + - - -
20C LEU* 3.7 25.4 - - + +
23C GLU* 2.7 36.4 + - - +
24C PRO 4.4 0.8 + - - -
25C VAL* 4.2 20.4 - - + +
119C ASN* 3.3 13.9 + - - +
120C VAL* 1.3 79.0 - - - +
122C THR* 1.3 63.8 + - + +
124C LEU* 3.6 4.5 + - - +
125C LEU* 3.2 42.0 + - + +
8G LEU 5.9 2.7 - - - -
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 4.1 6.5 - - - +
117C THR 5.6 1.6 - - - +
118C GLN* 3.4 22.0 + - - +
119C ASN* 2.5 48.4 + - - +
121C ARG* 1.3 76.8 - - + +
123C ILE* 1.3 57.1 + - - +
125C LEU* 3.4 8.6 + - + +
126C SER* 2.5 35.0 + - - -
8G LEU* 4.7 28.5 - - + +
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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
----------------------------------------------------------
62C LEU* 4.8 12.6 - - + -
68C TYR* 5.6 0.4 - - - +
73C PRO* 3.7 33.2 - - + -
75C PHE* 5.1 2.9 - - + -
94C ILE* 4.8 1.0 - - + +
96C ILE* 4.2 17.5 - - + -
97C LEU* 3.8 30.7 - - + -
114C TRP* 4.1 8.5 - - + -
119C ASN 3.1 17.1 + - - +
120C VAL* 3.1 17.6 + - + +
122C THR* 1.3 76.3 + - - +
124C LEU* 1.3 74.2 + - + +
126C SER* 3.0 9.5 + - - -
127C VAL* 2.9 31.5 + - + +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.4 12.3 - - + -
25C VAL* 4.2 27.6 - - + -
28C PHE* 3.8 34.5 - - + -
30C VAL* 5.4 8.1 - - + -
43C VAL* 5.0 6.3 - - + -
62C LEU* 4.7 5.8 - - + -
75C PHE* 4.6 15.9 - - + -
120C VAL* 2.9 37.8 + - + +
121C ARG 3.9 4.3 - - - +
123C ILE* 1.3 86.7 - - + +
125C LEU* 1.3 63.1 + - - +
127C VAL* 3.2 9.0 + - + +
128C ILE* 3.1 26.8 + - - +
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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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25C VAL* 3.8 32.8 - - + -
121C ARG* 3.2 34.8 + - + +
122C THR* 3.8 7.6 - - + +
123C ILE 3.2 0.2 - - - -
124C LEU* 1.3 80.1 - - - +
126C SER* 1.3 60.9 + - - +
128C ILE* 3.4 11.5 + - + +
129C SER* 3.2 21.0 + - - -
6G LYS 5.9 1.1 - - - +
7G THR 6.5 0.2 - - - -
8G LEU* 6.0 4.5 - - - -
44G ILE* 5.2 7.7 - - + +
68G HIS* 4.3 25.4 - - + +
69G LEU 4.5 5.4 - - - +
70G VAL* 3.7 30.4 - - + +
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 3.8 23.3 - - - +
96C ILE* 4.2 12.9 - - - +
122C THR* 2.5 22.7 + - - -
123C ILE* 3.0 9.8 + - - -
125C LEU* 1.3 74.1 - - - +
127C VAL* 1.3 60.4 + - - +
129C SER* 3.4 8.2 + - - -
130C LEU* 3.0 27.9 + - - +
70G VAL* 4.5 11.0 - - - +
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Residues in contact with VAL 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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28C PHE* 4.3 12.3 - - + -
75C PHE* 4.5 33.9 - - + -
77C PHE* 5.2 3.8 - - + -
92C VAL* 5.3 4.3 - - + -
94C ILE* 3.8 20.2 - - + -
97C LEU* 6.3 0.9 - - + -
123C ILE* 2.9 28.3 + - + +
124C LEU* 3.3 11.7 - - + +
126C SER* 1.3 76.2 - - - +
128C ILE* 1.3 55.7 + - - +
130C LEU* 3.1 4.4 + - + +
131C LEU* 2.8 57.2 + - + +
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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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25C VAL* 3.8 22.4 - - + -
26C GLU 4.4 4.0 - - - +
28C PHE* 3.5 32.1 - - + -
124C LEU 3.1 12.8 + - - +
125C LEU* 3.6 13.9 - - + +
127C VAL* 1.3 75.2 - - - +
129C SER* 1.3 60.3 + - - +
131C LEU* 3.4 7.6 + - - +
132C ASN* 2.6 46.1 + - - +
201C U94 4.1 12.1 - - + -
44G ILE* 3.8 25.4 - - + -
47G GLY* 3.9 18.6 - - - +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU 3.2 11.0 + - - -
126C SER* 3.5 10.1 - - - -
127C VAL 3.2 0.2 - - - -
128C ILE* 1.3 79.9 - - - +
130C LEU* 1.3 51.9 + - - +
132C ASN* 3.0 3.7 + - - +
133C GLU* 2.6 34.3 + - - +
42G ARG* 4.0 5.9 - - - +
44G ILE* 4.8 2.7 - - - +
49G GLN* 2.5 28.0 + - - -
70G VAL* 4.3 14.9 - - - +
72G ARG* 3.2 29.0 + - - +
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Residues in contact with LEU 130 (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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83C HIS* 3.0 24.6 + - + -
85C ASN* 3.5 34.1 - - + +
86C ILE* 6.2 0.7 - - + -
92C VAL* 4.0 10.1 - - + -
93C CYS 3.4 14.4 - - - +
94C ILE* 3.4 33.7 - - + -
126C SER 3.0 17.7 + - - +
127C VAL* 3.6 6.5 - - + +
129C SER* 1.3 76.0 - - - +
131C LEU* 1.3 63.8 + - + +
133C GLU 3.3 16.2 - - - -
135C ASN* 4.0 19.3 - - + +
72G ARG* 3.5 12.5 - - - +
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Residues in contact with LEU 131 (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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28C PHE* 5.1 4.9 - - + -
45C ILE* 5.3 1.1 - - + -
53C TYR* 4.8 8.4 - - + +
77C PHE* 4.7 15.7 - - + -
81C MET* 5.6 4.0 - - + -
83C HIS* 3.7 32.4 + - + +
86C ILE* 4.8 13.0 - - + -
127C VAL* 2.8 39.4 + - + +
128C ILE* 3.7 7.6 - - - +
130C LEU* 1.3 78.5 - - + +
132C ASN* 1.3 63.6 + - - +
134C PRO* 4.5 2.6 - - - +
201C U94 3.4 60.5 - - + +
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Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ILE* 2.6 37.8 + - - +
129C SER 3.5 5.2 - - - +
131C LEU* 1.3 76.9 - - - +
133C GLU* 1.3 59.7 + - - +
134C PRO* 3.7 6.6 - - - +
148C TYR* 3.8 8.3 + - - -
201C U94 3.1 46.6 + - + +
47G GLY 3.5 17.6 + - - -
48G LYS* 3.7 1.6 + - - +
49G GLN* 3.0 47.2 + - + +
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Residues in contact with GLU 133 (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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129C SER 2.6 9.7 + - - +
130C LEU* 3.3 5.0 - - - +
132C ASN* 1.3 75.0 - - - +
134C PRO* 1.3 68.3 - - + +
148C TYR* 4.8 1.3 - - - -
42G ARG* 3.5 37.6 + - - -
49G GLN* 3.1 24.7 + - - +
72G ARG* 2.1 51.0 + - - +
74G ARG 3.9 10.9 - - - +
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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