Contacts of the helix formed by residues 125 - 142 (chain C) in PDB entry 3HYW
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 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 4.1 25.6 - - - +
45C PHE* 3.8 9.6 - - - -
109C LEU* 4.1 13.7 - - + -
123C ILE 4.0 0.9 - - - +
124C CYS* 1.3 82.9 - - - +
126C ALA* 1.3 58.6 + - - +
127C GLU* 3.5 16.0 + - - +
128C HIS* 3.0 41.6 + - + +
129C ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TYR* 3.9 12.1 + - + +
45C PHE* 3.6 22.2 - - + -
48C LEU* 3.9 20.4 - - + -
55C PHE* 3.8 29.2 - - + -
125C THR* 1.3 73.7 - - - +
127C GLU* 1.3 59.6 + - - +
129C ALA* 3.3 1.5 + - - +
130C LEU* 3.0 37.6 + - + +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 3.3 28.1 + - - +
38C TYR* 2.6 32.1 + - - -
125C THR* 3.5 11.0 - - - +
126C ALA* 1.3 78.3 + - - +
128C HIS* 1.3 63.1 + - + +
130C LEU* 3.5 8.8 + - + +
131C GLU* 3.2 31.0 + - - +
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Residues in contact with HIS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.1 11.2 - - + +
111C PHE* 4.1 21.7 - + - -
117C GLU* 5.3 7.9 - - + -
122C SER* 3.1 35.9 + - - +
125C THR* 3.0 41.5 + - + +
127C GLU* 1.3 74.6 - - + +
129C ALA* 1.3 59.9 + - - +
131C GLU* 3.3 23.5 + - - +
132C THR* 3.0 30.0 + - - -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.6 24.0 - - + +
48C LEU* 4.0 13.0 - - + -
49C ALA* 3.4 19.5 - - + +
122C SER 3.7 7.1 + - - -
123C ILE* 4.3 7.4 - - - +
125C THR 2.9 18.4 + - - +
126C ALA* 3.5 6.3 - - - +
127C GLU 3.3 0.2 - - - -
128C HIS* 1.3 78.2 - - - +
130C LEU* 1.3 61.5 + - - +
132C THR* 3.1 5.2 + - - -
133C GLN 3.1 18.2 + - - -
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.9 34.3 - - + +
55C PHE* 4.7 20.2 - - + +
126C ALA* 3.0 24.8 + - + +
127C GLU* 3.9 7.9 - - + +
129C ALA* 1.3 76.5 - - - +
131C GLU* 1.3 62.1 + - + +
133C GLN* 3.4 17.0 + - + +
134C LYS* 3.4 23.2 + - - +
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 5.4 1.3 - - + -
127C GLU* 3.2 18.2 + - - +
128C HIS* 3.3 34.6 + - - +
129C ALA 3.2 0.2 - - - -
130C LEU* 1.3 74.8 - - + +
132C THR* 1.3 63.3 + - - +
134C LYS* 3.3 23.2 + - - +
135C LYS* 3.3 25.7 + - + +
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Residues in contact with THR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA* 4.0 9.6 - - + -
121C THR* 3.4 34.0 - - - +
122C SER 2.7 28.6 + - - -
123C ILE* 4.2 3.4 - - + -
128C HIS 3.0 4.6 + - - -
129C ALA 3.1 9.4 + - - -
131C GLU* 1.3 74.0 - - - +
133C GLN* 1.3 60.2 + - - +
135C LYS* 3.1 4.2 + - - +
136C LEU* 2.8 30.1 + - + +
163C PHE* 3.9 27.1 - - + -
247C PHE* 3.9 6.3 - - + -
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Residues in contact with GLN 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU 4.2 4.7 - - - +
49C ALA 3.0 27.4 + - - +
50C MET* 3.3 13.1 + - - +
51C GLY* 3.9 18.5 - - - -
129C ALA 3.1 10.4 + - - +
130C LEU* 3.6 15.7 - - + +
131C GLU 3.3 0.4 - - - -
132C THR* 1.3 76.3 - - - +
134C LYS* 1.3 63.4 + - + +
136C LEU* 3.1 9.8 + - - +
137C GLN* 2.8 55.8 + - + +
140C TYR* 4.9 2.3 + - - -
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Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU* 3.5 19.5 - - - +
131C GLU* 3.3 21.1 + - + +
132C THR 3.2 0.8 - - - -
133C GLN* 1.3 76.4 - - + +
135C LYS* 1.3 65.1 + - + +
137C GLN* 3.3 17.7 + - - +
138C GLU* 3.3 12.0 + - - +
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Residues in contact with LYS 135 (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 17.3 - - + -
131C GLU 3.3 12.8 + - - +
132C THR 3.1 7.5 + - - +
134C LYS* 1.3 77.3 - - + +
136C LEU* 1.3 59.9 + - - +
138C GLU* 3.2 33.6 + - - +
139C LEU* 3.1 23.7 + - - +
247C PHE* 3.9 22.4 - - + -
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Residues in contact with LEU 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 3.3 25.8 - - - +
50C MET* 3.9 13.5 - - - -
132C THR* 2.8 15.2 + - + +
133C GLN* 3.1 10.3 + - - +
135C LYS* 1.3 74.9 - - - +
137C GLN* 1.3 59.4 + - - +
139C LEU* 2.9 28.8 + - + +
140C TYR* 2.9 35.9 + - + +
163C PHE* 3.8 20.0 - - + -
167C LEU* 3.7 27.8 - - + -
247C PHE* 3.5 29.2 - - + -
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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
----------------------------------------------------------
133C GLN* 2.8 43.4 + - + +
134C LYS* 3.3 11.2 + - - +
136C LEU* 1.3 75.3 - - - +
138C GLU* 1.3 60.7 + - - +
140C TYR* 3.6 25.1 + - - +
141C ALA* 3.3 22.9 + - - +
174C ARG* 3.8 14.6 + - - +
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Residues in contact with GLU 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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134C LYS 3.3 7.3 + - - +
135C LYS* 3.2 45.8 + - - +
136C LEU 3.1 0.2 - - - -
137C GLN* 1.3 78.7 - - - +
139C LEU* 1.3 57.5 + - - +
141C ALA* 3.6 4.9 + - - +
142C ASN* 2.8 33.8 + - - +
246C LYS* 4.1 21.3 + - - +
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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
----------------------------------------------------------
135C LYS 3.1 11.5 + - - +
136C LEU* 2.9 31.4 + - + +
138C GLU* 1.3 74.8 - - - +
140C TYR* 1.3 64.6 + - + +
142C ASN 3.1 3.7 - - - +
143C PRO* 3.1 35.2 - - + +
144C GLY 3.7 34.5 - - - +
146C VAL* 3.7 25.8 - - + -
167C LEU* 4.3 12.1 - - + -
171C LEU* 4.4 11.9 - - + -
176C ILE* 4.9 0.2 - - - +
180C VAL* 4.5 2.9 - - + -
246C LYS* 4.5 8.5 - - + +
247C PHE* 4.2 17.9 - - + -
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Residues in contact with TYR 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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50C MET* 3.6 19.1 + - - +
133C GLN* 4.9 2.0 + - - -
136C LEU* 2.9 42.0 + - + +
137C GLN* 3.6 31.6 - - - +
138C GLU 3.4 0.2 - - - -
139C LEU* 1.3 81.2 - - + +
141C ALA* 1.3 63.0 + - - +
142C ASN 3.6 0.2 + - - -
143C PRO* 3.9 5.5 - - - +
167C LEU* 4.0 10.5 - - + +
170C GLU* 3.5 25.5 - - + +
171C LEU* 3.9 29.6 - - + -
174C ARG* 3.4 42.8 - - - +
176C ILE* 3.8 22.2 - - + +
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN 3.3 14.2 + - - +
138C GLU* 3.9 6.7 - - - +
139C LEU 3.3 0.4 - - - -
140C TYR* 1.3 80.5 - - - +
142C ASN* 1.3 68.8 + - - +
143C PRO* 3.9 3.9 - - - +
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Residues in contact with ASN 142 (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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138C GLU* 2.8 19.0 + - - +
139C LEU* 3.1 6.0 - - - +
141C ALA* 1.3 84.4 - - - +
143C PRO* 1.3 70.6 - - - +
246C LYS* 2.7 48.3 + - - +
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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
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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