Contacts of the helix formed by residues 121 - 138 (chain C) in PDB entry 5WJ9
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 THR 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ALA 3.8 0.2 - - - -
120C TYR* 1.3 81.2 + - - +
122C ARG* 1.3 57.9 + - - +
123C GLU* 3.5 26.2 - - + +
124C GLN* 3.2 15.5 + - + +
125C LEU* 2.8 36.0 + - - +
103D HIS 5.3 1.9 + - - -
104D LEU* 4.1 11.4 - - - +
135D GLN* 4.9 3.5 + - - +
142D VAL* 3.4 29.0 - - + +
144D LEU* 3.4 5.6 - - - -
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 1.3 70.8 - - - +
123C GLU* 1.3 53.8 + - - +
125C LEU* 3.3 4.9 + - - +
126C TYR* 2.8 46.0 + - + -
225C PHE* 3.2 57.7 - - + +
140D PRO 3.2 21.6 + - - -
141D ASP* 3.4 17.9 + - - +
142D VAL* 2.7 17.4 + - - +
143D SER 2.9 23.9 + - - +
144D LEU* 3.5 10.9 - - - +
145D GLY 4.6 7.7 + - - -
146D ARG* 5.1 9.5 - - - +
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Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 4.0 16.9 - - + +
122C ARG* 1.3 81.3 - - - +
124C GLN* 1.3 56.9 + - + +
126C TYR* 3.4 13.2 - - + +
127C GLN* 2.8 50.8 + - - +
142D VAL* 5.3 5.7 - - - +
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Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 5.4 0.5 - - - +
118C ALA 4.2 6.0 + - - +
119C ALA* 3.1 31.4 - - - +
120C TYR* 2.9 29.3 + - - +
121C THR* 3.4 21.9 + - + +
122C ARG 3.2 0.8 - - - -
123C GLU* 1.3 80.4 - - + +
125C LEU* 1.3 53.4 + - - +
127C GLN* 3.4 15.8 + - - +
128C ALA* 2.8 31.3 + - - +
273C ILE* 4.7 6.5 - - - +
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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
----------------------------------------------------------
119C ALA* 3.7 17.5 - - + -
121C THR 2.8 19.7 + - - +
122C ARG 3.5 3.8 - - - +
124C GLN* 1.3 71.9 - - - +
126C TYR* 1.3 60.4 + - - +
128C ALA* 3.1 3.8 + - - +
129C ILE* 2.8 48.3 + - + +
223C LEU* 4.1 7.4 - - + -
225C PHE* 3.8 16.8 - - + -
228C LEU* 4.8 1.1 - - + -
231C VAL* 6.0 0.4 - - + -
262C PHE* 3.2 40.6 - - + -
271C ILE* 3.7 23.8 - - + -
144D LEU* 3.7 21.5 - - + -
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Residues in contact with TYR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ARG* 2.8 39.5 + - + -
123C GLU* 3.4 13.2 - - - +
125C LEU* 1.3 72.0 - - - +
127C GLN* 1.3 52.1 + - + +
129C ILE* 3.2 8.4 + - + +
130C PHE* 2.8 70.2 + + + -
221C LEU* 3.4 21.3 + - + -
222C THR* 3.5 25.3 - - - +
223C LEU* 3.4 24.4 + - + -
225C PHE* 3.6 26.8 - + - -
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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
----------------------------------------------------------
107C LEU* 3.8 21.6 - - + +
123C GLU* 2.8 40.8 + - - +
124C GLN* 3.5 13.1 - - - +
126C TYR* 1.3 69.8 - - + +
128C ALA* 1.3 60.9 - - - +
130C PHE* 3.7 9.5 - - + +
131C HIS* 2.8 32.6 + - - +
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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
----------------------------------------------------------
105C PHE 4.9 3.5 - - - +
106C LEU* 5.6 0.3 - - - -
107C LEU* 4.3 21.3 + - + +
117C PHE* 6.2 0.2 - - + -
124C GLN* 2.8 20.0 + - - +
125C LEU* 3.3 11.7 - - - +
127C GLN* 1.3 73.8 - - - +
129C ILE* 1.3 61.1 + - - +
131C HIS* 3.4 2.6 + - - +
132C ALA* 3.3 21.3 + - - +
262C PHE* 3.6 23.9 - - + -
273C ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 2.8 41.7 + - + +
126C TYR* 3.6 7.2 - - + +
128C ALA* 1.3 73.4 - - - +
130C PHE* 1.3 66.7 + - + +
131C HIS 3.4 0.2 + - - -
132C ALA* 3.5 5.9 + - - +
133C VAL* 3.3 21.1 + - - +
165C LEU* 4.2 27.4 - - + -
221C LEU* 4.2 12.1 - - + -
223C LEU* 3.7 30.3 - - + -
231C VAL* 4.5 11.2 - - + -
233C ILE* 3.9 8.6 - - + +
262C PHE* 3.5 28.9 - - + -
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Residues in contact with PHE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 2.8 62.2 + + + +
127C GLN* 4.0 9.2 - - + +
129C ILE* 1.3 74.7 - - + +
131C HIS* 1.3 59.1 + - - +
133C VAL* 3.4 5.5 + - + +
134C ASP* 2.8 41.2 + - - +
218C TYR* 3.5 34.4 - + - -
219C LYS* 3.6 42.0 - - - +
221C LEU* 4.6 11.7 - - + -
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Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C HIS 5.2 2.2 + - - -
104C LEU 2.9 26.4 + - - -
106C LEU 3.7 7.5 + - - -
107C LEU* 3.5 54.4 - - + +
127C GLN 2.8 23.0 + - - +
128C ALA 3.6 4.9 - - - +
129C ILE 3.3 0.2 - - - -
130C PHE* 1.3 69.1 - - - +
132C ALA* 1.3 57.5 + - - +
134C ASP* 3.5 9.3 + - - +
135C GLN* 2.8 62.3 + - + +
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Residues in contact with ALA 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PHE* 3.6 34.2 + - - +
128C ALA 3.3 7.0 + - - +
129C ILE 3.6 9.2 - - - +
131C HIS* 1.3 79.1 - - - +
133C VAL* 1.3 57.1 + - - +
136C TYR* 2.8 30.4 + - - +
163C LEU* 5.1 2.0 - - - +
233C ILE* 3.7 24.0 - - + -
235C PHE* 5.6 1.1 - - + -
260C ILE* 3.9 14.6 - - + -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 3.3 16.5 + - + +
130C PHE 3.8 5.2 - - - +
131C HIS 3.3 0.2 - - - -
132C ALA* 1.3 72.1 - - - +
134C ASP* 1.3 56.0 + - - +
136C TYR* 3.3 1.4 + - - +
137C LEU* 2.8 37.9 + - + +
163C LEU* 3.6 30.7 - - + -
165C LEU* 4.0 25.8 - - + -
195C VAL* 4.6 3.4 - - + -
218C TYR* 3.2 47.1 - - + +
233C ILE* 4.7 6.3 - - + -
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Residues in contact with ASP 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 2.8 37.4 + - - +
131C HIS* 3.5 10.9 + - - +
133C VAL* 1.3 71.5 - - - +
135C GLN* 1.3 63.4 + - + +
137C LEU* 3.2 8.3 + - - +
138C ALA* 2.8 31.9 + - - +
218C TYR* 3.7 15.7 + - - -
219C LYS* 4.6 8.3 + - - -
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Residues in contact with GLN 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.9 3.4 + - - -
103C HIS 5.1 1.0 + - - -
104C LEU* 3.3 45.8 + - + +
105C PHE* 3.6 24.4 - - + -
131C HIS* 2.8 44.3 + - + +
134C ASP* 1.3 74.0 - - + +
136C TYR* 1.3 63.1 + - - +
138C ALA* 3.5 4.4 - - - +
139C LEU* 3.2 25.8 + - - +
142C VAL* 3.8 27.3 - - - +
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Residues in contact with TYR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PHE* 3.7 7.8 - - + -
132C ALA 2.8 19.5 + - - +
133C VAL 3.5 4.0 - - - +
135C GLN* 1.3 76.4 - - - +
137C LEU* 1.3 65.0 + - + +
139C LEU* 3.6 5.5 - - + +
149C TYR* 2.7 64.2 + + - +
150C VAL* 4.8 1.4 + - - +
162C GLY* 3.3 12.5 - - - -
163C LEU* 3.3 50.4 + - + -
195C VAL* 4.1 3.6 - - + -
196C ASP 4.8 0.4 - - - -
197C PRO* 3.7 23.7 - - + +
235C PHE* 3.6 46.7 - + + -
236C ARG 5.1 2.2 + - - -
237C LEU* 4.6 2.0 - - + -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 2.8 24.6 + - + +
134C ASP* 3.5 6.7 - - - +
136C TYR* 1.3 81.9 - - + +
138C ALA* 1.3 58.1 + - + +
139C LEU 3.5 2.4 + - - -
140C PRO* 4.7 2.4 - - - +
141C ASP* 5.5 0.3 - - - +
149C TYR* 4.0 4.9 + - - -
195C VAL* 4.3 19.7 - - + -
196C ASP 4.7 0.7 - - - +
197C PRO* 4.3 29.6 - - + +
198C PRO* 4.8 13.0 - - + +
216C SER* 5.7 1.6 - - - +
218C TYR* 3.1 36.6 - - + +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP 2.8 18.6 + - - +
135C GLN* 3.5 7.8 - - - +
137C LEU* 1.3 71.5 - - + +
139C LEU* 1.3 59.7 + - - +
140C PRO* 3.8 1.8 - - - -
141C ASP* 3.9 17.4 - - + +
142C VAL* 3.2 35.7 + - + +
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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