Contacts of the helix formed by residues 105 - 120 (chain C) in PDB entry 3ESF
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 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C ILE* 4.0 5.1 - - - +
100C ARG* 4.1 21.7 - - - +
103C PHE* 3.2 10.1 + - - +
104C GLY* 1.3 80.5 - - - +
106C PHE* 1.3 62.6 + - - +
107C ALA* 3.7 9.8 + - - +
108C LYS* 3.1 24.3 + - - +
109C PHE* 3.3 17.7 + - - +
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Residues in contact with PHE 106 (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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89C GLY 4.0 4.7 - - - -
90C GLU* 3.4 45.1 - - + +
91C PRO* 3.5 31.9 - - + -
99C ILE* 3.9 14.6 - - + +
100C ARG* 4.4 8.5 - - + +
105C SER* 1.3 70.7 - - - +
107C ALA* 1.3 61.3 + - - +
109C PHE* 3.2 18.2 + + - +
110C LYS* 2.9 46.1 + - + +
183C TRP* 4.5 14.6 - + - -
188C TRP* 3.7 26.9 - + - -
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Residues in contact with ALA 107 (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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105C SER* 3.3 9.7 + - - +
106C PHE* 1.3 81.9 - - - +
108C LYS* 1.3 55.7 + - - +
110C LYS* 3.4 9.7 + - - +
111C GLU* 2.9 29.8 + - - +
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Residues in contact with LYS 108 (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 PHE* 3.5 26.2 - - + +
105C SER* 3.1 20.5 + - - +
107C ALA* 1.3 73.1 - - - +
109C PHE* 1.3 60.6 + - - +
111C GLU* 3.3 36.4 + - - +
112C GLU* 2.9 33.7 + - + +
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Residues in contact with PHE 109 (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 ILE* 3.8 17.3 - - + -
103C PHE* 3.5 48.5 - + + +
105C SER 3.3 3.8 + - - +
106C PHE* 3.2 24.1 + + - +
108C LYS* 1.3 77.3 - - - +
110C LYS* 1.3 65.1 + - - +
112C GLU* 3.1 2.4 + - - +
113C PHE* 2.8 50.6 + + + +
128C LEU* 3.9 32.1 - - + -
139C VAL* 4.0 6.7 - - + -
158C LEU* 5.3 3.4 - - + -
183C TRP* 3.6 33.2 - + - -
188C TRP* 4.0 16.8 - + - -
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Residues in contact with LYS 110 (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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106C PHE* 2.9 38.3 + - + +
107C ALA* 3.5 11.7 - - - +
109C PHE* 1.3 72.1 - - - +
111C GLU* 1.3 56.1 + - - +
114C THR* 2.7 41.3 + - - +
180C GLN* 4.6 13.1 - - - +
183C TRP* 3.6 62.8 - - + +
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Residues in contact with GLU 111 (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 ALA 2.9 14.1 + - - +
108C LYS* 3.4 42.3 + - - +
109C PHE 3.2 0.2 - - - -
110C LYS* 1.3 77.9 - - - +
112C GLU* 1.3 57.7 + - - +
114C THR* 3.7 3.7 - - - -
115C ASN* 2.9 51.9 + - - +
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Residues in contact with GLU 112 (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 PHE* 3.5 22.1 - - - -
108C LYS* 2.9 19.8 + - + +
109C PHE* 3.7 4.0 - - - +
111C GLU* 1.3 78.3 - - - +
113C PHE* 1.3 60.8 + - - +
115C ASN* 3.4 6.9 + - - +
116C ALA* 3.1 23.1 + - + +
138C LYS* 5.8 0.9 - - - +
139C VAL* 3.7 32.8 + - + +
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Residues in contact with PHE 113 (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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109C PHE* 2.8 42.1 + + + +
112C GLU* 1.3 70.9 - - - +
114C THR* 1.3 61.6 + - - +
116C ALA* 3.2 2.8 + - - +
117C ALA* 2.9 30.6 + - + +
126C ALA* 3.6 33.6 - - + +
127C TRP 3.7 24.9 - - - -
128C LEU* 3.8 4.7 - - + -
139C VAL* 3.8 12.3 - - + +
158C LEU* 4.8 5.6 - - + -
159C THR* 4.7 1.1 - - - -
160C CYS* 3.8 21.8 - - + -
179C VAL* 5.3 2.2 - - + -
182C PHE* 3.9 27.1 - + - -
183C TRP* 3.5 29.6 - + + -
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Residues in contact with THR 114 (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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110C LYS* 2.7 26.4 + - - +
111C GLU* 3.7 5.2 - - - -
113C PHE* 1.3 76.4 - - - +
115C ASN* 1.3 66.6 + - - +
117C ALA* 3.2 0.7 + - - -
118C VAL* 2.8 46.4 + - + +
179C VAL* 4.2 16.4 - - + -
180C GLN* 4.3 11.6 + - - +
183C TRP* 2.9 20.8 + - - -
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Residues in contact with ASN 115 (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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111C GLU* 2.9 43.7 + - - +
112C GLU* 3.8 6.5 - - - +
113C PHE 3.2 0.2 - - - -
114C THR* 1.3 84.9 - - - +
116C ALA* 1.3 57.4 + - - +
118C VAL* 4.5 3.4 - - - +
119C GLY* 2.9 27.9 + - - +
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Residues in contact with ALA 116 (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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112C GLU 3.1 17.9 + - - +
113C PHE 3.5 4.5 - - - +
115C ASN* 1.3 77.3 - - - +
117C ALA* 1.3 58.5 + - - +
119C GLY* 5.2 0.2 - - - -
120C HIS* 3.0 32.1 + - - +
126C ALA* 4.4 6.2 - - + +
139C VAL* 3.7 20.4 - - + -
141C GLN* 3.6 36.2 - - + +
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Residues in contact with ALA 117 (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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113C PHE* 2.9 24.6 + - + +
114C THR 3.8 2.2 - - - +
116C ALA* 1.3 79.7 - - - +
118C VAL* 1.3 50.9 + - - +
126C ALA* 3.9 19.9 - - + +
160C CYS* 5.0 2.2 - - - -
162C VAL* 3.5 16.4 - - + +
175C ARG* 2.7 37.1 + - - -
179C VAL* 3.7 26.5 - - + -
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Residues in contact with VAL 118 (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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114C THR* 2.8 33.1 + - + +
115C ASN* 4.5 3.6 - - - +
117C ALA* 1.3 72.7 - - - +
119C GLY* 1.3 63.0 + - - +
120C HIS 4.4 0.2 - - - +
175C ARG* 3.4 19.0 + - - +
176C PRO* 4.0 39.0 - - + +
179C VAL* 3.8 24.2 - - + -
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Residues in contact with GLY 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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115C ASN 2.9 20.1 + - - -
116C ALA* 3.9 0.9 - - - -
118C VAL* 1.3 78.8 - - - +
120C HIS* 1.3 65.0 + - - +
121C PHE* 3.1 7.1 + - - +
141C GLN* 5.0 1.1 - - - -
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Residues in contact with HIS 120 (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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116C ALA 3.0 17.2 + - - +
118C VAL 3.4 2.3 - - - +
119C GLY* 1.3 75.7 - - - +
121C PHE* 1.3 69.0 + - - +
122C GLY 3.7 4.2 - - - +
123C SER 3.4 4.2 + - - -
124C GLY* 3.7 22.4 - - - -
125C TRP 4.8 2.2 + - - +
126C ALA* 6.4 0.2 - - + -
141C GLN* 2.8 32.1 + - + +
142C THR 3.3 25.8 + - - -
143C HIS* 3.0 29.6 + - + -
162C VAL* 4.0 11.9 - - + -
175C ARG* 2.7 40.1 + - - +
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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