Contacts of the helix formed by residues 123 - 140 (chain C) in PDB entry 3A5Z
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C HIS 4.1 0.8 + - - -
122C TYR* 1.3 76.8 - - - +
124C MET* 1.3 65.1 + - - +
125C TYR* 2.6 44.0 + - + +
126C ARG* 3.0 18.6 + - - +
127C LEU* 3.1 18.4 + - - +
234C GLU* 6.1 0.4 - - - +
250C HIS* 3.9 12.8 - - + +
295C SER* 3.5 6.8 + - - -
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Residues in contact with MET 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASP* 1.3 75.9 - - - +
125C TYR* 1.3 101.4 + - + +
127C LEU* 3.3 5.5 + - - +
128C MET* 3.0 33.8 + - + +
213C TYR* 3.6 17.7 - - + -
214C HIS* 3.5 21.8 - - + +
234C GLU* 3.6 44.1 + - - +
235C ARG 3.6 12.3 - - - -
236C PHE* 3.8 14.8 - - + -
250C HIS* 4.2 14.7 - - + +
295C SER* 3.7 8.4 + - - -
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ASP* 2.6 22.8 + - + +
124C MET* 1.3 92.7 - - + +
126C ARG* 1.3 64.7 + - - +
128C MET* 3.2 20.0 + - + +
129C ASN* 3.1 31.5 + - - +
213C TYR* 3.6 20.7 - + - -
214C HIS* 3.0 33.0 + - - -
228C GLU* 5.7 0.7 + - - -
234C GLU* 4.6 6.1 - - - -
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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
----------------------------------------------------------
121C HIS 4.8 6.2 + - - -
122C TYR* 3.4 60.8 + - + +
123C ASP* 3.0 24.5 + - - +
125C TYR* 1.3 77.5 - - - +
127C LEU* 1.3 61.7 + - - +
129C ASN* 3.6 12.4 + - + +
130C GLU* 3.4 15.8 + - - +
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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
----------------------------------------------------------
117C TRP* 3.5 34.1 - - + +
119C ARG* 4.1 19.1 - - + -
122C TYR* 4.2 5.6 - - + -
123C ASP 3.1 11.9 + - - +
124C MET 3.6 7.9 - - - +
125C TYR 3.1 0.6 - - - -
126C ARG* 1.3 75.9 - - - +
128C MET* 1.3 66.3 + - - +
130C GLU* 2.9 17.4 + - - +
131C VAL* 3.0 11.9 + - + +
236C PHE* 4.2 12.6 - - + -
249C PHE 4.8 0.4 - - - +
295C SER* 3.7 13.9 - - - +
296C GLY 3.5 43.3 - - - +
297C VAL* 3.9 11.2 - - + -
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Residues in contact with MET 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C MET* 3.0 48.8 + - + +
125C TYR* 3.5 32.5 - - + +
127C LEU* 1.3 77.0 - - - +
129C ASN* 1.3 60.4 + - - +
131C VAL* 2.9 8.8 + - - +
132C ASP* 2.8 25.9 + - - +
146C SER* 5.5 2.5 - - - -
211C PHE* 3.4 35.2 - - + -
213C TYR* 4.1 12.8 - - + -
236C PHE* 3.5 38.8 - - + -
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Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C TYR* 3.1 22.1 + - - +
126C ARG* 3.7 14.2 - - + +
127C LEU 3.1 0.2 - - - -
128C MET* 1.3 79.4 - - - +
130C GLU* 1.3 58.2 + - - +
132C ASP* 3.1 14.4 + - - +
133C ASP* 3.0 32.1 + - - +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.8 8.7 - - + -
30C PHE* 4.5 2.3 - - - -
33C ARG* 2.7 37.9 + - - +
117C TRP* 3.1 29.7 + - + +
119C ARG* 2.9 40.6 + - - +
122C TYR* 4.7 7.8 + - + -
126C ARG 3.4 9.4 + - - +
127C LEU* 2.9 13.6 + - + +
129C ASN* 1.3 75.2 - - - +
131C VAL* 1.3 66.1 + - - +
133C ASP* 3.3 9.4 + - - +
134C LEU* 3.1 21.3 + - - +
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 3.7 29.6 - - + -
127C LEU 3.0 17.6 + - - +
128C MET* 2.9 13.3 + - - +
130C GLU* 1.3 73.1 - - - +
132C ASP* 1.3 60.8 + - - +
134C LEU* 3.3 5.3 + - - +
135C LEU* 2.9 43.0 + - + +
211C PHE* 3.4 21.8 - - + -
236C PHE* 4.4 6.3 - - + -
238C VAL* 4.3 11.0 - - + -
246C ALA* 5.1 2.2 - - + -
297C VAL* 4.2 18.6 - - + -
299C LEU* 5.0 6.7 - - + -
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C MET 2.8 11.5 + - - +
129C ASN* 3.2 20.1 + - - +
131C VAL* 1.3 76.3 - - - +
133C ASP* 1.3 67.8 + - - +
134C LEU 3.3 0.2 + - - -
135C LEU* 3.3 6.4 + - - +
136C GLN* 3.0 52.9 + - - +
142C PRO 4.5 0.2 - - - +
143C ALA* 3.9 5.5 - - - +
144C ALA* 3.1 43.8 + - - +
209C PRO* 5.5 0.7 - - - +
211C PHE* 4.0 9.3 - - + -
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Residues in contact with ASP 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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29C PHE* 3.8 7.6 - - + -
33C ARG* 2.9 30.8 + - - +
129C ASN* 3.0 19.9 + - - +
130C GLU* 3.3 8.5 + - - +
132C ASP* 1.3 78.2 - - - +
134C LEU* 1.3 62.1 + - - +
136C GLN* 3.9 11.3 + - - +
137C GLN* 3.0 27.0 + - - +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE* 4.3 17.7 - - + -
29C PHE* 3.6 41.9 - - + -
30C PHE* 4.6 4.9 - - + -
115C LEU* 3.6 30.1 - - + -
117C TRP* 4.1 14.6 - - + -
130C GLU 3.1 12.6 + - - +
131C VAL* 3.5 9.2 - - - +
132C ASP 3.2 0.2 - - - -
133C ASP* 1.3 77.7 - - - +
135C LEU* 1.3 64.8 + - + +
137C GLN* 3.0 4.9 - - + +
138C VAL* 2.9 32.3 + - + +
299C LEU* 4.1 17.3 - - + -
304C LEU* 5.0 6.7 - - + -
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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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131C VAL* 2.9 29.7 + - + +
132C ASP* 3.8 6.1 - - - +
134C LEU* 1.3 77.9 - - + +
136C GLN* 1.3 56.4 + - - +
138C VAL* 5.1 1.1 - - - -
139C LEU* 2.7 46.6 + - + +
141C CYS* 4.1 7.4 - - - -
209C PRO* 3.9 20.0 - - + -
211C PHE* 4.8 4.0 - - + -
238C VAL* 3.8 30.1 - - + -
245C LEU* 4.1 23.1 - - + -
299C LEU* 4.2 19.1 - - + -
304C LEU* 4.1 18.8 - - + -
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Residues in contact with GLN 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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132C ASP* 3.0 34.4 + - - +
133C ASP* 3.9 9.4 + - - +
135C LEU* 1.3 74.7 - - - +
137C GLN* 1.3 58.4 + - - +
140C ASP* 2.7 31.7 + - - -
141C CYS* 3.9 19.9 + - - +
142C PRO 3.9 12.8 - - - +
143C ALA* 3.0 36.2 - - - +
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Residues in contact with GLN 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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25C GLU* 3.0 33.5 + - - +
28C ARG* 6.3 1.0 - - - +
29C PHE* 4.0 24.9 - - + +
133C ASP 3.0 17.3 + - - +
134C LEU* 3.0 13.0 - - - +
136C GLN* 1.3 78.6 - - - +
138C VAL* 1.3 62.9 + - + +
140C ASP* 4.2 4.3 + - - +
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Residues in contact with VAL 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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22C ILE* 4.1 24.6 - - + +
25C GLU* 3.3 31.4 - - + +
26C ILE* 4.3 20.2 - - + +
134C LEU* 2.9 30.7 + - + +
135C LEU 4.2 0.4 - - - +
137C GLN* 1.3 74.8 - - + +
139C LEU* 1.3 62.6 + - - +
140C ASP* 3.4 1.8 + - - +
304C LEU* 4.3 25.1 - - + -
308C ALA* 4.5 16.6 - - + +
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Residues in contact with LEU 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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135C LEU* 2.7 31.5 + - + +
138C VAL* 1.3 71.7 - - - +
140C ASP* 1.3 69.6 + - - +
141C CYS* 3.3 19.6 + - + +
209C PRO* 4.7 1.6 - - + -
240C TYR* 3.6 33.0 - - + -
245C LEU* 4.6 6.1 - - + -
304C LEU* 3.9 24.7 - - + -
307C LEU* 4.0 11.2 - - + -
308C ALA* 3.7 38.4 - - + +
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Residues in contact with ASP 140 (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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136C GLN 2.7 24.5 + - - -
137C GLN 5.0 3.6 - - - +
138C VAL 3.4 3.2 - - - +
139C LEU* 1.3 75.5 - - - +
141C CYS* 1.3 60.4 + - - +
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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
------------------------------------------------------------
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