Contacts of the helix formed by residues 121 - 134 (chain C) in PDB entry 4IXU
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 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C PHE* 3.3 18.4 - - - -
36C GLY* 3.7 5.9 - - - -
92C VAL* 3.7 19.9 - - - +
96C ASN* 2.9 17.9 + - - -
119C ASP* 2.7 22.0 + - - -
120C HIS* 1.3 77.4 - - - +
122C LEU* 1.3 62.6 + - - +
123C ALA 3.1 0.4 - - - -
124C ILE* 3.1 15.8 + - - +
159C LEU* 4.0 23.3 - - - -
160C HIS* 3.7 7.0 - - - +
163C PRO* 4.4 5.4 - - - -
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Residues in contact with LEU 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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31C ALA* 3.8 18.6 - - + +
33C PHE* 3.7 24.2 - - + -
96C ASN* 3.2 10.1 - - - +
99C LEU* 3.6 4.4 - - + +
115C THR* 3.9 10.8 - - + +
116C LEU 4.5 0.2 - - - +
117C GLY* 3.5 31.4 - - - +
118C GLY 4.0 1.8 - - - -
119C ASP 3.2 18.9 + - - +
120C HIS 3.0 1.0 - - - -
121C SER* 1.3 80.9 + - - +
123C ALA* 1.3 66.3 + - - +
124C ILE 3.1 0.4 - - - -
125C GLY* 3.0 4.2 + - - -
126C THR* 3.0 38.4 + - + +
293C ASP* 4.3 7.0 - - - +
295C VAL* 3.9 19.3 - - + -
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Residues in contact with ALA 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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120C HIS* 3.0 23.6 + - + +
122C LEU* 1.3 78.7 - - - +
124C ILE* 1.3 65.9 + - - +
126C THR* 3.5 10.1 - - - -
127C ILE* 3.0 30.2 + - + +
141C TRP* 3.6 30.5 - - + -
163C PRO* 4.5 1.8 - - + -
167C LEU* 3.9 2.4 - - - +
249C SER* 3.9 9.2 - - - +
293C ASP* 4.0 4.5 - - - +
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Residues in contact with ILE 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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92C VAL* 4.7 3.8 - - + -
96C ASN* 3.8 12.8 - - + +
121C SER* 3.4 18.4 - - - +
122C LEU 3.1 0.2 - - - -
123C ALA* 1.3 77.9 - - - +
125C GLY* 1.3 56.2 + - - +
128C SER* 2.8 39.2 + - - +
159C LEU* 5.2 2.7 - - + +
163C PRO* 3.7 27.8 - - + +
166C PHE* 3.7 26.7 - - + -
167C LEU* 3.8 14.3 - - + +
181C PHE* 3.8 16.8 - - + -
183C TRP* 4.3 6.5 - - + -
184C ILE* 3.5 31.6 - - + -
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Residues in contact with GLY 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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96C ASN* 2.9 44.2 + - - -
99C LEU* 4.5 2.7 - - - -
100C ALA* 3.3 19.2 - - - +
122C LEU 3.0 0.4 + - - -
124C ILE* 1.3 76.1 - - - +
126C THR* 1.3 59.3 - - - +
129C GLY 2.9 25.5 + - - -
183C TRP* 4.3 1.1 - - - -
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Residues in contact with THR 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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99C LEU* 3.7 16.8 - - + -
103C VAL* 3.6 18.6 - - + +
115C THR* 3.4 24.0 - - - +
122C LEU* 3.0 17.0 + - + +
123C ALA* 3.5 8.5 - - - -
125C GLY* 1.3 75.6 - - - +
127C ILE* 1.3 60.3 + - - +
130C HIS* 2.9 31.0 + - - +
247C HIS* 3.4 7.9 - - - -
291C ALA* 6.0 0.7 - - - -
293C ASP* 2.8 38.4 + - - +
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Residues in contact with ILE 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 ALA* 3.0 18.6 + - + +
126C THR* 1.3 76.6 - - - +
128C SER* 1.3 57.2 + - - +
130C HIS* 3.4 3.4 + - - +
131C ALA* 2.8 28.8 + - - +
137C LEU* 4.5 5.4 - - + -
139C VAL* 4.2 17.9 - - + -
141C TRP* 3.8 24.0 - - + -
167C LEU* 3.6 26.2 - - + -
187C CYS* 4.1 4.7 - - - -
188C ILE* 4.0 31.9 - - + -
193C ILE* 6.2 0.2 - - + -
247C HIS* 3.4 35.2 - - + +
293C ASP* 4.9 0.2 - - - +
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Residues in contact with SER 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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100C ALA* 4.3 1.6 - - - -
124C ILE* 2.8 25.2 + - - +
125C GLY 3.8 2.0 - - - -
127C ILE* 1.3 77.3 - - - +
129C GLY* 1.3 61.5 + - - +
131C ALA* 3.3 2.6 + - - +
132C ARG* 3.2 28.7 + - - +
167C LEU* 3.7 13.2 - - - +
183C TRP* 3.8 27.7 - - - -
184C ILE* 4.5 7.1 - - - +
185C LYS 4.9 3.4 + - - -
187C CYS* 4.2 12.3 - - - -
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Residues in contact with GLY 129 (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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100C ALA* 3.3 29.8 - - - +
103C VAL* 3.9 7.0 - - - -
104C SER* 3.5 17.3 - - - -
107C VAL* 5.4 0.5 - - - +
125C GLY 2.9 14.7 + - - -
126C THR 4.0 0.9 - - - -
128C SER* 1.3 76.8 - - - +
130C HIS* 1.3 63.0 + - - +
132C ARG* 3.4 19.0 - - - +
133C HIS* 4.1 2.6 + - - +
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Residues in contact with HIS 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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103C VAL* 3.6 9.7 - - + +
107C VAL* 4.1 15.9 - - + +
126C THR 2.9 20.1 + - - +
127C ILE 3.6 4.3 - - - +
129C GLY* 1.3 77.7 - - - +
131C ALA* 1.3 60.9 + - - +
132C ARG 3.2 0.9 + - - -
133C HIS* 3.4 3.6 + - - +
134C CYS* 2.8 46.2 + - + +
137C LEU* 3.5 16.7 - - + +
245C PRO* 4.3 2.0 - - + +
246C ILE 3.9 10.1 - - - -
247C HIS* 2.9 28.7 + - + +
290C SER* 2.8 39.5 + - - -
291C ALA* 3.4 17.6 - - + +
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Residues in contact with ALA 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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127C ILE 2.8 21.7 + - - +
128C SER 3.8 2.9 - - - +
130C HIS* 1.3 71.9 - - - +
132C ARG* 1.3 65.6 + - - +
134C CYS 3.5 5.2 - - - +
135C PRO* 3.2 27.9 - - + +
137C LEU* 3.4 18.6 - - + +
187C CYS* 3.6 34.8 - - + +
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Residues in contact with ARG 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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97C GLN* 5.1 3.2 + - - +
100C ALA* 3.8 28.3 + - - +
101C GLU* 3.7 22.2 + - - +
104C SER* 3.9 18.1 - - - +
128C SER* 3.2 16.5 + - - +
129C GLY* 3.4 11.4 - - - +
130C HIS 3.1 0.6 - - - -
131C ALA* 1.3 79.7 - - - +
133C HIS* 1.3 64.8 + - + +
134C CYS 3.8 0.2 + - - -
135C PRO* 4.8 3.3 - - - +
183C TRP* 3.6 36.0 + - - -
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Residues in contact with HIS 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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104C SER* 2.8 51.4 + - - -
105C ARG* 5.4 0.2 - - - -
107C VAL* 4.3 18.4 - - + -
108C SER* 3.6 23.2 + - - -
129C GLY 4.1 0.6 + - - +
130C HIS 3.4 3.0 + - - +
132C ARG* 1.3 80.8 + - + +
134C CYS* 1.3 64.3 + - - +
135C PRO* 3.5 8.3 - - - +
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Residues in contact with CYS 134 (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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107C VAL* 3.8 16.2 - - - -
130C HIS* 2.8 40.8 + - + +
131C ALA* 3.3 6.9 + - - -
133C HIS* 1.3 86.2 - - - +
135C PRO* 1.3 68.0 - - - +
136C ASP 3.2 2.9 - - - -
137C LEU* 3.1 22.0 + - + +
245C PRO* 4.3 19.1 - - + -
290C SER* 4.3 4.5 - - - -
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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