Contacts of the helix formed by residues 118 - 138 (chain C) in PDB entry 1YE2
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 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA 4.0 13.5 - - - +
116C GLU* 2.9 10.3 + - - +
117C PHE* 1.3 75.1 - - - +
119C PRO* 1.3 71.9 - - - +
120C ALA* 3.5 6.1 + - - +
121C VAL* 3.0 28.5 + - + +
122C HIS* 2.8 27.0 + - - +
30D ARG* 3.6 2.0 - - - +
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Residues in contact with PRO 119 (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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118C THR* 1.3 88.2 - - - +
120C ALA* 1.3 60.5 + - - +
122C HIS* 3.7 2.5 - - + +
123C ALA* 3.2 22.2 + - - +
26D GLU* 5.7 0.2 - - + -
30D ARG* 3.8 31.6 - - + +
33D VAL* 3.8 17.8 - - + +
34D VAL* 4.5 2.3 - - + +
51D PRO* 4.7 5.2 - - + -
55D MET* 3.7 46.7 - - + -
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 3.7 12.3 + - - +
118C THR* 3.2 6.5 + - - +
119C PRO* 1.3 79.1 - - - +
121C VAL* 1.3 59.2 + - + +
123C ALA* 3.4 8.0 + - - +
124C SER* 3.1 29.3 + - - -
33D VAL* 4.8 0.4 - - - -
51D PRO* 4.2 25.4 - - + +
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN* 4.2 30.3 - - + +
13C ALA* 4.0 26.2 - - + -
116C GLU 3.4 24.2 - - - +
117C PHE* 4.6 2.9 - - - -
118C THR* 3.0 26.6 + - + +
120C ALA* 1.3 77.4 - - + +
122C HIS* 1.3 59.7 + - - +
124C SER* 3.2 2.1 + - - -
125C LEU* 2.9 38.7 + - + +
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Residues in contact with HIS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.5 13.7 - - + +
117C PHE* 3.4 28.9 - + + -
118C THR 2.8 16.9 + - - +
119C PRO* 3.7 5.6 - - + +
121C VAL* 1.3 77.0 - - - +
123C ALA* 1.3 63.2 + - - +
125C LEU* 3.7 2.4 - - - +
126C ASP* 3.0 19.7 + - + +
30D ARG* 3.2 35.9 + - - +
34D VAL* 3.8 26.3 - - + +
35D PHE* 6.0 0.6 - - - -
109D VAL* 4.7 14.8 - - + +
112D CYS* 3.9 33.7 - - + -
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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
----------------------------------------------------------
141A ARG* 4.5 0.9 + - - -
6C ASP* 5.1 0.2 - - - -
119C PRO 3.2 11.7 + - - +
120C ALA* 3.5 10.5 - - - +
121C VAL 3.2 0.4 - - - -
122C HIS* 1.3 80.5 - - - +
124C SER* 1.3 61.6 + - - +
126C ASP* 3.3 3.1 + - - +
127C LYS* 3.0 31.0 + - + +
33D VAL* 4.1 24.7 - - + +
34D VAL* 3.9 19.7 - - + +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 4.5 2.1 - - - +
6C ASP* 2.9 37.9 + - - -
9C ASN* 2.9 43.7 + - - -
10C VAL* 3.9 5.5 - - - +
120C ALA 3.1 7.6 + - - -
121C VAL 3.2 4.0 + - - -
123C ALA* 1.3 76.9 - - - +
125C LEU* 1.3 58.4 + - - +
127C LYS* 3.4 3.8 + - - +
128C PHE* 2.8 29.8 + - - +
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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
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10C VAL* 3.9 31.4 - - + +
13C ALA* 4.2 13.5 - - + -
14C TRP* 5.6 7.0 - - + -
106C LEU* 3.7 15.7 - - + -
109C LEU* 3.8 30.3 - - + -
113C LEU* 6.5 0.2 - - + -
117C PHE* 4.3 17.9 - - + -
121C VAL* 2.9 36.6 + - + +
122C HIS 3.7 1.3 - - - +
124C SER* 1.3 73.9 - - - +
126C ASP* 1.3 61.3 + - - +
128C PHE* 3.6 8.6 - - + +
129C LEU* 2.9 38.2 + - + +
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.6 38.6 + - - +
102C SER* 6.2 0.3 - - - -
106C LEU* 3.4 27.0 - - + +
122C HIS* 3.0 18.4 + - + +
123C ALA 3.6 4.5 - - - +
124C SER 3.2 0.2 - - - -
125C LEU* 1.3 79.0 - - - +
127C LYS* 1.3 61.4 + - - +
129C LEU* 3.9 3.0 - - - +
130C ALA* 3.0 21.8 + - - +
34D VAL* 3.8 14.3 - - + +
35D PHE* 3.7 14.7 - - - -
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Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.9 68.4 + - + +
1C VAL 2.8 30.5 + - - +
2C LEU* 4.1 7.4 - - + -
3C SER* 4.2 2.8 + - - +
6C ASP* 2.7 35.9 + - - +
123C ALA* 3.0 17.3 + - + +
124C SER* 3.6 7.0 - - - +
126C ASP* 1.3 74.5 - - - +
128C PHE* 1.3 60.1 + - - +
130C ALA* 3.3 3.1 + - - +
131C SER* 2.9 34.1 + - - +
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Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LEU* 3.9 26.2 - - + +
10C VAL* 3.7 27.6 - - + -
14C TRP* 6.0 4.7 - + - -
66C LEU* 4.5 8.5 - - + -
69C ALA* 3.9 12.6 - - + -
70C VAL* 3.8 28.5 - - + -
73C VAL* 4.1 13.5 - - + -
76C MET* 3.9 21.3 - - + -
124C SER 2.8 22.3 + - - +
125C LEU* 3.3 8.9 + - + +
127C LYS* 1.3 73.0 - - - +
129C LEU* 1.3 77.9 + - + +
131C SER* 3.2 4.5 + - - -
132C VAL* 2.9 45.7 + - + +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TRP* 6.5 0.7 - - + -
66C LEU* 4.3 19.5 - - + -
102C SER* 3.7 40.0 + - - +
105C LEU* 4.2 28.5 - - + -
106C LEU* 3.9 20.2 - - + +
109C LEU* 5.2 5.4 - - + -
125C LEU* 2.9 24.7 + - + +
126C ASP* 4.0 3.4 - - - +
128C PHE* 1.3 92.0 - - + +
130C ALA* 1.3 57.8 + - - +
132C VAL* 3.4 6.1 + - + +
133C SER* 3.0 32.6 + - - -
142C HEM 5.2 3.8 - - + +
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.1 15.7 - - - +
102C SER* 5.3 1.1 - - - -
126C ASP* 3.0 17.8 + - - +
127C LYS* 3.5 5.2 - - - +
129C LEU* 1.3 76.6 - - - +
131C SER* 1.3 62.5 + - - +
133C SER* 3.2 7.9 + - - -
134C THR* 2.9 27.6 + - - -
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Residues in contact with SER 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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1C VAL* 5.6 3.1 + - - -
2C LEU* 4.1 14.9 + - - +
76C MET* 4.3 19.1 - - - -
127C LYS* 2.9 15.6 + - - +
128C PHE* 3.4 10.1 - - - -
130C ALA* 1.3 77.0 - - - +
132C VAL* 1.3 61.8 + - - +
134C THR* 3.3 8.7 + - - -
135C VAL* 3.0 28.1 + - - +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.5 10.8 - - + -
69C ALA* 4.4 7.9 - - + -
76C MET* 3.8 17.0 - - - -
80C LEU* 4.5 9.6 - - + +
128C PHE* 2.9 45.4 + - + +
129C LEU* 3.6 11.0 - - - +
130C ALA 3.3 0.2 - - - -
131C SER* 1.3 73.5 - - - +
133C SER* 1.3 63.8 + - - +
135C VAL* 3.3 6.9 + - - +
136C LEU* 3.0 41.1 + - + +
142C HEM 4.2 19.5 - - + -
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Residues in contact with SER 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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98C PHE* 3.5 36.9 + - - +
99C LYS* 5.5 1.5 - - - -
102C SER* 3.5 14.7 + - - -
129C LEU 3.0 18.5 + - - -
130C ALA* 3.5 7.6 - - - -
131C SER 3.2 0.2 - - - -
132C VAL* 1.3 78.1 - - - +
134C THR* 1.3 62.5 + - - +
136C LEU* 3.1 1.9 + - - +
137C THR* 3.0 30.8 + - - +
142C HEM 5.0 4.7 - - - +
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Residues in contact with THR 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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134A THR* 6.2 4.0 - - + -
130C ALA* 2.9 13.9 + - - +
131C SER* 3.5 10.4 - - - -
133C SER* 1.3 77.1 - - - +
135C VAL* 1.3 65.4 + - + +
137C THR* 3.2 8.4 + - - -
138C SER* 3.1 27.1 + - - -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C MET* 4.3 20.6 - - + -
77C PRO* 3.9 35.2 - - + +
80C LEU* 4.0 21.8 - - + -
84C SER* 2.9 24.7 + - - +
131C SER* 3.0 15.9 + - - +
132C VAL* 3.3 7.2 + - - +
134C THR* 1.3 76.6 - - + +
136C LEU* 1.3 61.4 + - - +
138C SER* 2.9 26.7 + - - +
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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
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80C LEU* 4.6 10.5 - - + -
83C LEU* 3.7 36.8 - - + +
84C SER* 3.6 29.0 - - - +
87C HIS* 4.1 10.1 - - + +
88C ALA* 5.1 0.2 - - - +
98C PHE* 3.8 17.5 - - + -
132C VAL* 3.0 24.6 + - + +
133C SER 3.1 4.7 + - - +
135C VAL* 1.3 76.7 - - - +
137C THR* 1.3 58.6 + - - +
138C SER 3.5 0.4 + - - -
139C LYS 5.1 0.2 + - - -
140C TYR* 3.5 14.4 - - - -
142C HEM 3.4 54.1 - - + -
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Residues in contact with THR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PRO* 4.3 20.6 - - + +
98C PHE* 3.4 39.0 - - + -
133C SER 3.0 18.0 + - - +
134C THR* 3.2 9.3 + - - -
136C LEU* 1.3 77.5 - - - +
138C SER* 1.3 62.9 + - - +
139C LYS 3.3 3.2 + - - -
140C TYR* 3.6 29.9 + - + +
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Residues in contact with SER 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL* 4.6 16.3 + - - +
84C SER* 4.7 0.2 - - - -
134C THR* 3.1 17.8 + - - -
135C VAL* 2.9 18.0 + - - +
136C LEU 3.5 0.2 - - - -
137C THR* 1.3 79.3 - - - +
139C LYS* 1.3 75.4 + - - +
140C TYR 3.4 0.8 + - - -
141C ARG 4.6 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
------------------------------------------------------------
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