Contacts of the helix formed by residues 111 - 128 (chain C) in PDB entry 3U8Z
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 GLN 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 2.8 27.7 + - - -
56C LEU* 3.8 1.9 - - - -
57C ARG* 2.8 59.9 + - - +
58C GLU* 3.2 23.2 + - + +
109C LEU 4.0 2.1 - - - -
110C VAL* 1.3 80.4 - - + +
112C GLU* 1.3 63.7 + - - +
113C ILE* 4.1 12.2 - - + +
114C THR* 3.3 24.2 + - - +
115C GLN* 3.4 9.2 + - - +
200C ARG* 3.7 3.9 + - - +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 5.1 2.4 - - - +
55A GLY* 4.1 7.0 - - - +
57A ARG* 3.0 33.3 + - - +
110C VAL 3.7 0.6 + - - -
111C GLN* 1.3 67.3 - - - +
113C ILE* 1.4 54.9 + - - +
115C GLN* 3.1 20.0 + - - +
116C HIS* 2.7 36.5 + - + +
198C ARG* 2.9 39.0 + - - -
200C ARG* 3.6 28.5 - - - +
201C ASP* 2.8 33.5 + - - +
204C GLU* 4.6 2.7 - - - +
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Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG 4.5 3.8 - - - +
53A THR 3.1 31.9 - - - +
55A GLY* 4.1 18.5 + - - +
54C LEU* 3.5 34.1 - - + +
55C GLY 4.2 0.4 - - - +
56C LEU* 3.9 25.8 - - + -
111C GLN* 4.1 17.5 - - + +
112C GLU* 1.4 77.9 - - - +
114C THR* 1.4 53.4 + - - +
116C HIS* 3.1 9.9 + - + +
117C LEU* 2.9 58.6 + - + +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.4 18.2 - - - +
58C GLU* 2.8 30.5 + - + +
61C PHE* 4.0 10.1 - - + -
62C PHE* 3.8 29.2 - - + -
109C LEU* 3.6 26.2 - - + -
111C GLN* 3.5 10.9 - - - +
112C GLU 3.3 0.4 - - - -
113C ILE* 1.4 75.0 - - - +
115C GLN* 1.4 56.4 + - - +
117C LEU* 3.4 1.6 + - - +
118C PHE* 3.0 37.2 + - + -
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.0 14.6 - - + +
111C GLN 3.4 9.1 + - - +
112C GLU* 3.3 16.0 - - - +
114C THR* 1.4 74.5 - - - +
116C HIS* 1.3 54.5 + - - +
118C PHE 3.4 0.7 + - - -
119C PHE* 2.8 35.2 + - - +
200C ARG* 3.3 31.1 + - - +
201C ASP 2.9 28.2 + - - +
202C GLU* 5.1 1.2 - - - +
204C GLU* 3.0 19.7 - - + +
205C MET* 3.4 44.9 - - + +
208C LEU* 3.7 6.1 - - + +
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Residues in contact with HIS 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 6.1 2.2 - - + +
52A ARG* 3.2 52.0 + - + +
53A THR* 4.1 13.4 + - - +
55A GLY* 6.1 0.2 - - - -
30C ASP* 4.7 5.6 + - - -
112C GLU* 2.7 19.0 + - + +
113C ILE* 3.4 17.9 - - + +
115C GLN* 1.3 73.4 - - - +
117C LEU* 1.3 67.1 + - + +
119C PHE* 3.2 4.3 + + - +
120C LEU* 3.1 55.9 + - + +
204C GLU* 2.8 36.2 + - - +
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Residues in contact with LEU 117 (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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53A THR 5.7 0.7 - - - +
28C THR* 4.8 16.8 - - + -
29C MET* 4.3 13.0 - - + +
54C LEU* 4.4 9.0 - - + -
56C LEU* 4.6 5.6 - - + -
62C PHE* 4.0 23.3 - - + -
96C PHE* 3.8 37.0 - - + +
113C ILE* 2.9 46.3 + - + +
114C THR* 3.8 4.0 - - - +
116C HIS* 1.3 81.2 - - + +
118C PHE* 1.3 61.3 + - - +
120C LEU* 3.6 7.8 + - + +
121C GLN* 3.2 25.3 + - - +
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Residues in contact with PHE 118 (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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61C PHE* 3.7 17.3 - + + -
62C PHE* 3.7 16.8 - + - -
98C ALA* 3.5 20.0 - - + -
100C PHE 3.2 27.4 - - - -
101C TYR* 3.7 24.2 - + - -
102C PRO* 3.6 20.2 - - + -
109C LEU* 3.7 36.3 - - + -
114C THR* 3.0 26.0 + - + +
115C GLN 3.8 3.1 - - - +
117C LEU* 1.3 73.7 - - - +
119C PHE* 1.3 65.3 + - - +
121C GLN* 3.2 5.0 + - + +
122C VAL* 2.9 31.2 + - + +
208C LEU* 3.9 9.6 - - + -
217C TYR* 4.9 2.7 - - - -
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLN 2.8 21.0 + - - +
116C HIS* 3.4 4.9 - + - +
118C PHE* 1.3 73.7 - - - +
120C LEU* 1.3 72.5 + - + +
122C VAL* 4.0 0.5 - - - +
123C LYS* 2.9 63.0 + - + +
145C ALA* 4.1 7.9 - - - -
148C ALA* 3.7 22.2 - - + -
149C LYS* 6.4 0.2 - - - -
204C GLU* 3.5 44.2 - - + -
207C TYR* 3.5 48.4 - + + -
208C LEU* 3.9 12.5 - - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.4 34.4 - - + +
30C ASP* 3.4 39.7 - - + +
116C HIS* 3.1 46.1 + - + +
117C LEU* 4.0 6.1 - - + +
118C PHE 3.3 0.2 - - - -
119C PHE* 1.3 92.7 - - + +
121C GLN* 1.3 65.3 + - - +
123C LYS* 3.9 16.3 - - - +
124C LYS* 3.1 18.4 + - - +
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.8 14.9 - - + +
62C PHE* 5.3 1.0 - - - -
97C LEU* 3.5 27.8 - - + +
98C ALA* 2.8 52.6 + - - +
101C TYR* 3.0 23.5 + - - +
117C LEU 3.2 17.0 + - - +
118C PHE* 3.8 5.2 - - + +
120C LEU* 1.3 79.2 - - - +
122C VAL* 1.3 62.2 + - + +
124C LYS* 3.5 4.7 + - - +
125C GLN* 3.3 35.6 + - - +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C TYR* 4.0 21.3 - - + -
118C PHE* 2.9 23.5 + - + +
119C PHE 4.1 0.9 - - - +
121C GLN* 1.3 71.6 - - + +
123C LYS* 1.3 59.8 + - - +
125C GLN* 3.1 12.5 + - - +
126C ILE* 3.0 30.1 + - + +
131C ILE* 4.2 7.0 - - + -
207C TYR* 4.4 4.0 - - + -
208C LEU* 3.9 15.3 - - + -
211C ALA* 3.6 31.4 - - + -
217C TYR* 3.7 28.0 - - + +
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Residues in contact with LYS 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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119C PHE* 2.9 55.0 + - + +
120C LEU* 3.9 17.3 + - - +
122C VAL* 1.3 75.2 - - - +
124C LYS* 1.3 57.5 + - - +
126C ILE* 3.1 2.6 + - - +
127C LEU* 2.9 56.8 + - + +
145C ALA* 3.9 19.5 - - + -
207C TYR* 3.3 24.0 - - + +
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Residues in contact with LYS 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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29C MET* 3.8 21.5 - - + -
120C LEU 3.1 17.6 + - - +
121C GLN 3.7 6.1 - - - +
122C VAL 3.3 0.2 - - - -
123C LYS* 1.3 75.9 - - - +
125C GLN* 1.4 58.3 + - + +
127C LEU* 3.9 6.4 - - + +
128C ASP* 2.8 70.0 + - - +
130C LYS* 5.0 6.3 - - - +
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Residues in contact with GLN 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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101C TYR* 3.0 32.0 + - - -
121C GLN* 3.3 27.8 + - - +
122C VAL* 3.1 12.6 + - - +
124C LYS* 1.4 75.1 - - + +
126C ILE* 1.3 62.3 + - - +
128C ASP* 4.5 1.6 - - - -
129C GLU 3.2 1.2 + - - -
130C LYS* 2.9 51.8 + - + +
131C ILE* 3.2 36.1 + - + +
218C GLY 5.4 1.4 + - - -
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Residues in contact with ILE 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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122C VAL* 3.0 24.7 + - + +
123C LYS 3.1 7.2 + - - +
125C GLN* 1.3 74.9 - - - +
127C LEU* 1.4 72.0 + - + +
129C GLU* 3.2 18.5 + - - +
131C ILE* 3.9 22.4 - - + +
133C CYS* 4.4 15.8 - - + +
138C SER* 5.6 5.4 - - - +
141C LEU* 3.9 22.4 - - + -
207C TYR* 3.5 21.8 - - + +
211C ALA* 4.7 3.6 - - + -
214C LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 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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123C LYS* 2.9 47.3 + - + +
124C LYS* 4.0 6.5 - - + +
126C ILE* 1.4 84.1 - - + +
128C ASP* 1.4 63.1 + - - +
129C GLU* 3.2 11.2 + - - +
142C ALA* 6.5 1.3 - - + -
207C TYR* 5.3 1.3 - - - +
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Residues in contact with ASP 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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124C LYS* 2.8 58.0 + - - +
125C GLN 4.2 1.3 - - - +
127C LEU* 1.4 75.1 - - - +
129C GLU* 1.3 70.6 + - - +
130C LYS* 3.5 38.0 + - + +
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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