Contacts of the helix formed by residues 105 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.0 6.2 - - - +
100B ARG* 4.1 22.4 - - - +
103B PHE* 3.2 6.9 + - - +
104B GLY* 1.3 80.3 - - - +
106B PHE* 1.3 63.8 + - - +
107B ALA* 3.5 9.7 + - - +
108B LYS* 3.1 23.0 + - - +
109B PHE* 3.2 21.0 + - - +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B GLY 3.9 10.8 - - - -
90B GLU* 3.6 37.2 - - + +
91B PRO* 3.4 33.4 - - + -
99B ILE* 3.9 14.9 - - + +
100B ARG* 4.5 8.1 - - + +
105B SER* 1.3 73.6 - - - +
107B ALA* 1.3 60.8 + - - +
109B PHE* 3.2 20.5 + + - +
110B LYS* 2.8 46.7 + - + -
183B TRP* 4.5 11.4 - + - -
188B TRP* 3.6 26.7 - + - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B SER* 3.3 9.9 + - - +
106B PHE* 1.3 81.3 - - - +
108B LYS* 1.3 58.0 + - - +
110B LYS* 3.3 8.7 + - - +
111B GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.5 28.5 - - + +
104B GLY 5.2 0.2 - - - -
105B SER* 3.1 16.4 + - - +
106B PHE 3.2 0.2 - - - -
107B ALA* 1.3 74.3 - - - +
109B PHE* 1.3 60.6 + - - +
111B GLU* 2.8 34.6 + - - +
112B GLU* 2.9 30.8 + - + +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 3.7 26.9 - - + -
103B PHE* 3.7 40.4 - + + +
105B SER 3.2 3.4 + - - -
106B PHE* 3.4 25.1 - + - +
108B LYS* 1.3 77.4 - - - +
110B LYS* 1.3 59.6 + - - +
112B GLU* 3.2 2.3 + - - +
113B PHE* 2.9 47.9 + + + +
128B LEU* 3.9 33.4 - - + -
139B VAL* 4.2 3.8 - - + -
158B LEU* 5.0 4.3 - - + -
183B TRP* 3.7 29.2 - + - -
188B TRP* 3.9 22.2 - + - -
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 2.8 42.8 + - + +
107B ALA* 3.6 8.1 - - - +
109B PHE* 1.3 73.4 - - - +
111B GLU* 1.3 57.4 + - - +
114B THR* 2.8 37.0 + - - +
180B GLN* 4.7 10.8 + - - +
183B TRP* 3.5 61.2 - - + +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 2.9 17.1 + - - +
108B LYS* 2.8 46.3 + - - +
110B LYS* 1.3 77.1 - - - +
112B GLU* 1.3 56.7 + - - +
114B THR* 3.7 3.9 - - - -
115B ASN* 2.9 51.5 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B PHE* 3.2 29.0 - - - -
108B LYS* 2.9 17.5 + - + +
109B PHE 3.7 4.0 - - - +
111B GLU* 1.3 77.3 - - - +
113B PHE* 1.3 58.2 + - - +
115B ASN* 3.4 6.8 + - + +
116B ALA* 3.0 28.8 + - - +
139B VAL* 3.8 26.1 + - + +
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 2.9 36.7 + + + +
112B GLU* 1.3 72.3 - - - +
114B THR* 1.3 61.6 + - - +
116B ALA* 3.3 2.6 + - - +
117B ALA* 2.9 32.1 + - + +
126B ALA* 3.6 27.9 - - + +
127B TRP 3.7 29.8 - - - -
128B LEU 4.3 0.2 - - - -
139B VAL* 3.8 12.3 - - + +
158B LEU* 3.5 28.0 - - + -
160B CYS* 3.8 16.4 - - + -
179B VAL* 5.4 2.0 - - + -
182B PHE* 3.8 20.6 - + - -
183B TRP* 3.4 29.4 - + + -
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LYS* 2.8 22.1 + - - +
111B GLU* 3.7 4.9 - - - -
113B PHE* 1.3 77.8 - - - +
115B ASN* 1.3 62.6 + - - +
117B ALA* 3.3 0.3 + - - -
118B VAL* 2.9 46.6 + - + +
179B VAL* 4.1 15.5 - - + -
180B GLN* 4.1 15.4 + - - +
183B TRP* 2.7 26.9 + - - +
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Residues in contact with ASN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 2.9 41.2 + - - +
112B GLU* 3.8 6.9 + - - +
114B THR* 1.3 82.3 - - - +
116B ALA* 1.3 55.9 + - - +
118B VAL* 4.8 3.8 - - - +
119B GLY* 2.9 29.1 + - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLU 3.0 17.7 + - - +
113B PHE 3.5 4.5 - - - +
115B ASN* 1.3 73.4 - - - +
117B ALA* 1.3 59.6 + - - +
119B GLY 5.5 0.2 - - - -
120B HIS* 3.0 31.9 + - - +
126B ALA* 4.5 5.6 - - + +
139B VAL* 3.6 22.0 - - + -
141B GLN* 3.6 34.6 - - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 2.9 27.2 + - + +
114B THR 3.8 2.2 - - - +
116B ALA* 1.3 72.9 - - - +
118B VAL* 1.3 58.4 + - - +
120B HIS 3.8 0.2 + - - -
126B ALA* 3.9 21.0 - - + +
160B CYS* 5.0 2.2 - - - -
162B VAL* 3.5 15.4 - - + +
175B ARG* 2.8 31.1 + - - -
179B VAL* 3.7 26.9 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B THR* 2.9 33.5 + - + +
115B ASN* 4.3 4.0 - - - +
117B ALA* 1.3 76.6 - - - +
119B GLY* 1.3 63.1 + - - +
120B HIS 4.3 0.5 - - - +
175B ARG* 3.4 20.6 + - - +
176B PRO* 4.0 37.5 - - + +
179B VAL* 3.9 19.7 - - + -
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASN 2.9 19.1 + - - -
116B ALA 3.9 0.7 - - - -
118B VAL* 1.3 79.3 - - - +
120B HIS* 1.3 62.9 + - - +
121B PHE* 3.2 7.3 + - - +
141B GLN* 5.0 1.1 - - - -
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 3.0 18.9 + - - +
118B VAL 3.4 2.5 - - - +
119B GLY* 1.3 74.5 - - - +
121B PHE* 1.3 67.0 + - - +
122B GLY 3.7 4.9 - - - -
123B SER 3.4 4.2 + - - -
124B GLY* 3.7 21.5 - - - -
125B TRP 4.8 2.0 + - - +
126B ALA* 6.4 0.4 - - + -
141B GLN* 2.8 32.5 + - + +
142B THR 3.3 26.1 + - - -
143B HIS* 2.9 30.9 + + + -
162B VAL* 3.9 12.1 - - + -
175B ARG* 2.7 39.3 + - - +
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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
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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