Contacts of the helix formed by residues 110 - 124 (chain A) in PDB entry 4KEU
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ASN 4.4 0.2 + - - -
109A ARG* 1.3 78.0 - - - +
111A ILE* 1.3 64.1 + - - +
112A ASP* 3.3 14.5 + - - +
113A GLU* 3.1 41.4 + - - +
114A ILE* 3.3 14.1 + - - +
151A LYS* 5.8 0.2 - - - -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A SER* 1.3 75.1 - - - +
112A ASP* 1.3 59.3 + - - +
114A ILE* 3.1 11.1 + - - +
115A ALA* 2.9 24.8 + - - +
151A LYS* 3.9 34.9 - - + +
154A ARG* 3.8 31.9 - - + -
155A ALA* 3.7 25.1 - - - +
158A ILE* 3.8 17.0 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A SER* 3.1 11.2 + - - +
111A ILE* 1.3 76.6 + - - +
113A GLU* 1.3 59.9 + - + +
115A ALA* 3.3 7.1 + - - +
116A ASP* 2.9 39.7 + - - +
158A ILE* 4.2 19.4 - - - +
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 4.8 1.2 + - - -
106A PHE* 5.9 1.1 - - + -
108A ASN 4.4 2.4 - - - +
109A ARG* 2.8 62.0 + - + +
110A SER* 3.1 27.2 + - - +
112A ASP* 1.3 76.2 - - - +
114A ILE* 1.3 62.8 + - + +
116A ASP* 3.3 24.5 + - - +
117A LEU* 3.4 14.2 + - - +
267C LYS* 4.6 8.1 + - - -
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 4.0 12.6 - - + -
102A LEU* 3.8 30.5 - - + -
106A PHE* 3.7 23.3 - - + -
109A ARG* 5.2 2.7 - - + +
110A SER 3.3 12.8 + - - +
111A ILE* 3.1 9.1 + - - +
113A GLU* 1.3 74.7 - - + +
115A ALA* 1.3 64.4 + - - +
117A LEU* 3.1 25.4 + - + +
118A PHE* 3.5 24.4 + - + -
151A LYS* 4.1 26.0 - - + -
152A VAL* 4.9 4.3 - - - +
155A ALA* 3.5 17.3 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE 2.9 13.2 + - - +
112A ASP* 3.3 8.5 + - - +
114A ILE* 1.3 76.6 - - - +
116A ASP* 1.4 57.7 + - - +
118A PHE* 3.1 8.4 + - - +
119A ILE* 2.9 34.9 + - + +
155A ALA* 3.5 22.6 - - - +
158A ILE* 3.5 35.7 - - + -
159A ALA* 4.5 1.5 - - - +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 2.9 30.3 + - - +
113A GLU* 3.4 15.3 - - - +
114A ILE 3.1 0.2 - - - -
115A ALA* 1.4 74.1 - - - +
117A LEU* 1.3 61.1 - - + +
119A ILE* 3.9 14.6 - - - +
120A HIS* 2.9 30.0 + - - +
38C HIS* 6.1 0.4 - - - -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 4.9 4.0 - - + +
106A PHE* 3.5 37.2 - - + -
113A GLU 3.5 15.0 - - - +
114A ILE* 3.1 11.2 + - + +
116A ASP* 1.3 77.2 - - + +
118A PHE* 1.3 64.3 + - + +
120A HIS* 3.3 7.0 + - - +
121A ASP* 3.2 16.5 + - - -
36C TRP* 3.4 46.7 + - + +
38C HIS* 4.2 12.3 - - + +
39C LEU* 3.9 36.8 - - + -
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.7 19.2 - - + +
95A GLY* 3.4 36.1 - - - -
96A ILE* 3.8 22.4 - - + -
114A ILE* 3.7 25.8 - - + -
115A ALA* 3.1 6.0 + - - +
117A LEU* 1.3 77.4 - - + +
119A ILE* 1.3 63.4 - - - +
121A ASP* 3.0 5.9 + - - +
122A ILE* 2.9 27.1 + - - +
136A VAL* 3.8 21.8 - - + -
152A VAL* 4.1 11.0 - - + -
155A ALA* 3.8 35.7 - - + -
156A ALA* 3.9 7.6 - - + -
159A ALA* 3.8 12.8 - - + -
36C TRP* 4.2 7.9 - + - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ALA 2.9 24.4 + - - +
116A ASP* 3.9 15.9 - - - +
118A PHE* 1.3 75.0 - - - +
120A HIS* 1.3 54.5 + - - +
122A ILE* 3.1 7.6 + - - +
123A LYS* 2.7 67.7 + - + +
158A ILE* 4.6 9.2 - - + -
159A ALA* 4.0 20.0 - - - -
162A GLU* 4.1 25.1 - - + -
163A THR* 4.4 7.2 - - + -
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Residues in contact with HIS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP 2.9 19.5 + - - +
117A LEU 3.5 4.9 - - - +
119A ILE* 1.3 77.2 - - - +
121A ASP* 1.4 66.4 + - - +
123A LYS* 5.2 0.2 - - - -
124A GLU* 2.7 62.2 + - + +
125A GLY 3.1 20.5 + - - -
127A GLN 5.5 2.6 + - - -
128A GLY 5.6 3.4 + - - -
36C TRP* 4.7 0.4 - + - -
38C HIS* 3.6 53.4 + + + +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 3.0 21.8 + - - -
94A THR* 2.5 36.6 + - - +
117A LEU 3.2 1.1 + - - -
118A PHE 3.0 5.2 + - - +
120A HIS* 1.4 88.9 - - - +
122A ILE* 1.4 60.6 + - - +
125A GLY* 3.5 18.2 + - - +
126A ILE* 4.0 9.6 - - + +
127A GLN 4.7 0.9 + - - -
132A LYS* 3.5 7.4 - - - -
133A ALA* 3.0 22.6 + - + -
35C GLN 4.6 0.9 - - - +
36C TRP* 3.0 29.7 + - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 4.1 2.2 - - + -
118A PHE 2.9 24.8 + - - +
119A ILE 3.1 4.9 + - - +
121A ASP* 1.4 78.3 - - - +
123A LYS* 1.3 59.7 + - + +
132A LYS* 3.4 23.7 - - - +
133A ALA* 3.8 27.7 - - + +
135A PHE 5.2 0.2 - - - +
136A VAL* 4.1 13.2 - - + -
159A ALA* 4.2 5.8 - - + -
163A THR* 3.5 47.8 - - + +
165A VAL* 3.6 29.4 - - + -
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ILE* 2.7 43.3 + - + +
122A ILE* 1.3 76.6 - - + +
124A GLU* 1.3 76.7 + - + +
132A LYS* 3.3 19.0 + - - +
162A GLU* 4.3 22.8 + - - +
163A THR* 4.1 19.1 - - + +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A HIS* 2.7 54.4 + - + +
123A LYS* 1.3 89.4 - - + +
125A GLY* 1.3 54.8 + - - +
129A THR 3.9 6.5 - - - +
130A LEU* 3.9 11.6 - - - +
132A LYS* 3.5 15.1 + - - -
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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