Contacts of the helix formed by residues 120 - 139 (chain C) in PDB entry 4UC5
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 ASP 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 5.1 2.9 - - - -
111C ASN 3.8 1.4 + - - -
113C PRO* 3.2 12.9 - - + +
114C HIS* 2.9 39.3 + - + +
118C THR* 3.4 5.2 + - - +
119C PHE* 1.3 70.6 - - - +
121C ILE* 1.3 52.8 + - - +
122C ASN* 4.1 5.7 + - - +
123C PHE* 3.2 27.9 + - - +
124C GLY 2.8 29.5 + - - -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 6.2 1.8 - - - -
18C LEU* 3.4 31.6 - - + -
110C ILE* 3.6 30.9 - - + +
111C ASN* 3.4 31.2 - - - +
119C PHE* 2.9 13.0 + - + +
120C ASP* 1.3 69.5 - - - +
122C ASN* 1.3 64.8 + - - +
125C LEU* 2.8 45.1 + - + +
212D LEU* 4.3 16.6 - - + -
222D ILE* 4.0 23.6 - - + -
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.9 23.8 + - + -
17C GLU 4.5 6.1 + - - -
18C LEU* 3.5 19.6 - - - +
19C LEU* 3.0 47.6 + - + +
24C HIS* 3.5 11.7 + - - -
120C ASP* 3.3 5.8 + - - +
121C ILE* 1.3 79.9 - - - +
123C PHE* 1.3 61.9 + - - +
125C LEU* 4.8 3.2 - - - +
126C ARG* 3.0 23.9 + - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 3.4 25.9 + + + +
113C PRO* 3.7 19.3 - - + -
114C HIS* 3.7 21.5 - + - -
120C ASP* 3.2 30.1 + - - +
122C ASN* 1.3 80.6 - - - +
124C GLY* 1.3 55.9 + - - +
126C ARG* 3.1 3.6 + - + +
127C GLN* 2.8 63.8 + - + +
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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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109C LEU* 3.3 23.9 - - - +
110C ILE* 3.4 19.4 + - - -
113C PRO* 3.6 8.6 - - - +
120C ASP 2.8 14.5 + - - -
121C ILE 3.2 0.4 + - - -
123C PHE* 1.3 73.1 - - - +
125C LEU* 1.3 57.6 + - - +
127C GLN* 3.3 3.0 + - - +
128C ALA* 2.9 30.3 + - - +
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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
----------------------------------------------------------
18C LEU* 4.3 11.0 - - + -
19C LEU 5.5 0.2 - - - +
24C HIS* 4.1 14.0 + - + +
110C ILE* 3.5 25.5 + - + -
121C ILE* 2.8 37.6 + - + +
122C ASN* 4.0 5.8 - - - +
124C GLY* 1.3 71.9 - - - -
126C ARG* 1.3 64.3 + - - +
128C ALA* 3.4 4.1 + - - +
129C ARG* 3.0 24.4 + - - +
151C THR* 4.5 8.7 - - + -
154C TYR* 3.9 54.2 - - + +
155C TYR* 4.3 16.1 - - + -
212D LEU* 5.3 1.8 - - + -
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Residues in contact with ARG 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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26A TYR* 3.8 20.4 - - + +
27A GLU* 2.6 34.8 + - - -
19C LEU* 4.0 15.4 - - - +
23C ALA* 4.0 3.8 + - - +
24C HIS* 2.9 45.3 + - - +
27C GLU* 3.5 21.2 - - - +
28C LEU* 3.6 22.4 - - + -
122C ASN 3.0 19.2 + - - +
123C PHE* 3.1 7.2 + - + +
125C LEU* 1.3 77.9 - - - +
127C GLN* 1.3 57.5 + - - +
129C ARG* 3.4 2.1 + - - +
130C SER* 3.0 28.0 + - - -
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Residues in contact with GLN 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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68C PRO* 3.7 31.4 - - + +
109C LEU* 3.4 31.4 - - + +
113C PRO* 3.9 10.7 + - - +
123C PHE* 2.8 44.4 + - + +
124C GLY 3.7 4.5 - - - +
126C ARG* 1.3 75.8 - - - +
128C ALA* 1.3 64.5 + - - +
130C SER* 3.2 7.0 + - - -
131C LEU* 2.9 26.3 + - - +
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Residues in contact with ALA 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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97C PHE* 3.4 39.5 - - + -
109C LEU* 5.2 1.7 - - + +
110C ILE* 3.9 15.5 - - + -
124C GLY 2.9 17.0 + - - +
125C LEU* 3.8 4.5 - - - +
127C GLN* 1.3 76.7 - - - +
129C ARG* 1.3 65.3 + - - +
131C LEU* 3.4 2.4 + - - +
132C LEU* 3.0 29.6 + - - +
155C TYR* 4.5 6.3 - - + -
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Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C HIS* 4.0 27.3 + - + -
25C LEU* 3.2 21.4 - - - +
28C LEU* 2.9 39.6 + - + -
30C ILE* 3.9 12.5 - - - +
125C LEU 3.0 17.9 + - - +
126C ARG* 3.8 5.6 - - - +
128C ALA* 1.3 77.9 - - - +
130C SER* 1.3 56.5 + - - +
132C LEU* 3.3 2.6 + - - +
133C LEU* 2.9 29.7 + - + +
154C TYR* 2.8 35.2 + - + +
155C TYR* 3.7 13.2 - - + +
157C ASP* 2.8 43.6 + - - -
158C LEU* 3.7 17.4 - - + +
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.6 22.2 - - - +
126C ARG* 3.0 19.8 + - - -
127C GLN* 3.6 9.0 - - - -
129C ARG* 1.3 75.9 - - - +
131C LEU* 1.3 58.9 + - - +
133C LEU* 3.6 4.8 - - - +
134C SER* 2.9 37.0 + - - -
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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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65C ILE* 3.7 29.8 - - + -
68C PRO* 4.3 19.7 - - + +
71C ALA* 4.0 18.2 - - + -
72C LEU* 3.9 26.5 - - + -
95C VAL* 4.2 16.4 - - + -
97C PHE* 4.5 5.8 - - + -
109C LEU* 5.4 0.9 - - + -
127C GLN 2.9 16.2 + - - +
128C ALA* 3.8 4.7 - - - +
130C SER* 1.3 78.0 - - - +
132C LEU* 1.3 57.9 + - + +
134C SER* 3.2 4.6 + - - -
135C LEU* 2.9 54.1 + - + +
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Residues in contact with LEU 132 (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 VAL* 3.7 23.3 - - + -
97C PHE* 4.2 11.9 - - + -
128C ALA 3.0 23.4 + - - +
129C ARG 3.8 2.7 - - - +
131C LEU* 1.3 74.8 - - - +
133C LEU* 1.3 62.8 + - - +
135C LEU* 3.4 4.8 + - + +
136C ASN* 2.8 32.1 + - - +
142C ALA* 3.6 28.9 - - + -
155C TYR* 3.6 43.3 - - + +
158C LEU* 3.9 13.7 - - + -
159C ILE* 3.8 17.0 - - + -
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Residues in contact with LEU 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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28C LEU* 4.1 33.2 - - + +
29C PRO 3.8 24.7 - - - +
30C ILE* 4.4 4.3 - - - -
31C SER* 4.3 6.5 - - - +
34C ALA* 4.2 15.3 - - + -
129C ARG 2.9 17.7 + - - +
130C SER* 3.6 4.7 - - - +
132C LEU* 1.3 74.7 - - - +
134C SER* 1.3 66.3 + - - +
136C ASN* 3.3 1.1 + - - -
137C ASN* 2.9 51.9 + - - +
158C LEU* 3.9 14.7 - - + +
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 3.8 24.4 - - - +
130C SER* 2.9 22.2 + - - -
131C LEU* 3.5 6.2 - - - -
133C LEU* 1.3 78.2 - - - +
135C LEU* 1.3 61.2 + - - +
137C ASN* 3.2 9.5 + - - +
138C MET* 3.1 27.5 + - - +
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Residues in contact with LEU 135 (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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71C ALA 4.4 3.4 - - - +
72C LEU* 4.3 12.1 - - + -
75C ALA* 3.3 34.1 - - + -
93C MET* 3.9 13.5 - - + -
95C VAL* 4.0 28.3 - - + -
131C LEU* 2.9 44.8 + - + +
132C LEU* 3.7 8.7 - - + +
133C LEU 3.2 0.2 - - - -
134C SER* 1.3 74.5 - - - +
136C ASN* 1.3 67.6 + - - +
138C MET* 3.0 15.0 + - - +
140C MET* 3.0 36.7 + - + +
142C ALA* 4.7 2.5 - - + -
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Residues in contact with ASN 136 (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 GLU* 4.8 2.4 - - - +
34C ALA* 3.7 29.2 + - + -
37C LEU* 3.3 28.2 - - + +
38C VAL* 3.6 20.6 - - - +
132C LEU* 2.8 31.0 + - - +
133C LEU* 3.9 2.2 - - - +
135C LEU* 1.3 78.2 - - - +
137C ASN* 1.3 61.0 + - - +
139C GLY* 3.1 10.2 + - - -
140C MET 3.7 5.6 - - - -
141C PRO* 3.8 11.1 - - - +
142C ALA* 4.6 6.7 - - - +
158C LEU* 3.0 31.5 + - - +
160C SER* 4.7 0.2 + - - -
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Residues in contact with ASN 137 (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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31C SER* 2.8 29.0 + - - -
33C GLU* 3.6 19.9 + - - +
34C ALA* 3.7 7.5 + - - +
133C LEU* 2.9 39.5 + - - +
134C SER* 3.6 8.3 - - - +
135C LEU 3.2 0.2 - - - -
136C ASN* 1.3 76.3 - - - +
138C MET* 1.3 59.9 + - - +
139C GLY 3.6 0.3 + - - -
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Residues in contact with MET 138 (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 LEU* 3.5 37.5 - - + +
75C ALA* 3.8 26.9 - - - +
76C GLU* 4.1 31.2 - - + +
79C LEU* 3.4 27.5 - - + +
134C SER* 3.1 11.7 + - - +
135C LEU* 3.0 22.4 + - - +
137C ASN* 1.3 77.2 - - - +
139C GLY* 1.3 55.8 + - - +
140C MET* 4.0 8.1 - - + +
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Residues in contact with GLY 139 (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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37C LEU* 3.6 12.9 - - - +
79C LEU* 3.4 11.3 - - - +
82C ARG* 3.2 24.8 + - - -
136C ASN 3.1 12.9 + - - -
137C ASN 3.3 1.2 + - - -
138C MET* 1.3 79.6 - - - +
140C MET* 1.3 59.0 + - - +
141C PRO* 3.5 2.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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