Contacts of the helix formed by residues 114 - 130 (chain D) in PDB entry 4IME
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C THR* 5.0 0.3 + - - -
112D LYS 3.5 2.8 + - - -
113D PHE* 1.3 76.7 - - - +
115D PHE* 1.3 66.3 + - - +
116D PRO* 3.6 12.6 - - - +
117D GLU* 2.9 36.4 + - - +
118D ILE* 3.0 22.5 + - - +
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D SER* 1.3 74.4 - - - +
116D PRO* 1.4 75.3 - - + +
118D ILE* 3.0 13.6 + - + +
119D LYS* 2.8 29.4 + - + -
146D ILE* 4.3 16.2 - - + -
150D GLN* 3.3 68.0 - - + +
153D GLU* 3.4 39.0 - - + -
154D LEU* 3.8 31.2 - - + -
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Residues in contact with PRO 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D SER* 3.6 13.7 - - - +
115D PHE* 1.4 100.7 - - + +
117D GLU* 1.3 56.9 + - + +
119D LYS* 3.4 5.6 + - + +
120D HIS* 2.9 29.8 + - - +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C PRO* 3.3 27.6 - - - +
272C MET* 4.0 4.8 - - - +
273C THR* 2.8 42.9 + - - +
108D PRO* 5.6 0.4 - - - -
112D LYS 4.7 0.5 - - - +
113D PHE* 3.3 20.1 - - + -
114D SER* 2.9 39.6 + - - +
116D PRO* 1.3 76.1 - - + +
118D ILE* 1.3 62.2 + - - +
120D HIS* 3.5 7.3 + - - +
121D TYR* 3.0 27.9 + - - +
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Residues in contact with ILE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D THR* 4.8 5.4 - - + -
108D PRO* 4.2 18.6 - - + +
113D PHE* 3.9 26.2 - - + +
114D SER 3.0 19.7 + - - +
115D PHE* 3.4 17.7 - - + +
117D GLU* 1.3 73.9 - - - +
119D LYS* 1.3 66.9 + - - +
121D TYR* 3.1 7.5 + - - +
122D TYR* 3.1 49.9 + - + -
144D VAL* 3.9 31.6 - - + -
146D ILE* 4.5 17.7 - - + -
154D LEU* 5.0 1.3 - - + -
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PHE* 2.8 27.6 + - + +
116D PRO* 3.9 6.5 - - + +
118D ILE* 1.3 73.7 - - - +
120D HIS* 1.3 57.2 + - - +
122D TYR* 3.2 4.0 + - - +
123D ASP* 2.9 54.3 + - - +
153D GLU* 3.0 49.6 + - + +
154D LEU* 3.7 27.3 + - + +
156D LYS* 4.6 12.6 - - - +
157D ASN* 4.6 3.4 - - - +
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Residues in contact with HIS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLU* 3.8 22.8 + - + +
271C PRO* 5.2 7.0 - - + -
272C MET 6.0 0.7 - - - -
274C LYS* 6.3 1.4 - - - +
85D LEU* 4.5 9.2 - - + -
116D PRO 2.9 18.0 + - - +
117D GLU* 3.7 8.1 - - - +
118D ILE 3.3 0.2 - - - -
119D LYS* 1.3 76.2 - - - +
121D TYR* 1.3 58.7 + - - +
123D ASP* 3.3 8.5 + - - +
124D SER* 2.8 54.6 + - - -
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Residues in contact with TYR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C PRO* 4.3 10.8 - - + -
81D GLY* 3.0 25.7 - - - -
82D SER 3.1 24.0 + - - -
85D LEU* 3.8 38.1 - - + +
88D ALA* 4.7 1.3 - - + -
105D ALA* 4.0 0.7 - - + -
106D VAL 2.7 29.6 + - - -
108D PRO* 3.6 27.1 - - + -
117D GLU 3.0 14.1 + - - +
118D ILE* 3.1 12.1 + - - +
120D HIS* 1.3 76.5 - - - +
122D TYR* 1.3 84.9 + + - +
124D SER* 3.3 1.7 + - - -
125D ILE* 3.2 46.5 + - + +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ALA* 2.7 39.4 + - + -
107D THR* 3.1 25.6 + - + +
118D ILE* 3.1 42.5 + - + -
119D LYS 3.7 4.7 - - - +
121D TYR* 1.3 90.4 - + - +
123D ASP* 1.3 65.1 + - - +
124D SER 3.2 0.3 + - - -
125D ILE* 3.3 5.4 + - + +
126D ILE* 3.0 36.7 + - + +
133D MET* 3.9 26.2 - - + +
135D VAL* 3.6 30.5 - - + +
136D TYR 4.0 0.2 + - - -
154D LEU* 4.0 25.1 - - + -
160D VAL* 5.4 4.5 - - + -
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Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LYS* 2.9 55.9 + - - +
120D HIS* 3.8 9.1 + - - +
122D TYR* 1.3 79.0 - - - +
124D SER* 1.3 58.5 + - - +
126D ILE* 3.8 2.1 - - - +
127D GLU* 2.9 30.3 + - - +
154D LEU* 5.0 1.4 - - - +
157D ASN* 3.0 32.6 + - - +
160D VAL* 5.6 0.3 - - - +
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C GLU* 4.6 2.3 + - - -
85D LEU* 4.0 19.4 - - - +
89D ILE* 4.2 9.8 - - - +
120D HIS* 2.8 47.0 + - - -
121D TYR 3.7 4.5 - - - -
122D TYR 3.1 0.4 - - - -
123D ASP* 1.3 74.9 - - - +
125D ILE* 1.3 66.5 + - - +
127D GLU* 3.4 4.8 + - - +
128D ALA* 3.0 26.2 + - - +
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Residues in contact with ILE 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D VAL* 4.4 9.2 - - + -
85D LEU* 3.7 14.6 - - + -
88D ALA* 3.8 28.9 - - + +
89D ILE* 4.2 9.6 - - + -
103D LEU* 4.1 17.3 - - + -
105D ALA* 4.0 15.5 - - + -
121D TYR* 3.2 39.1 + - + +
122D TYR* 3.3 5.1 + - - +
124D SER* 1.3 74.6 - - - +
126D ILE* 1.3 61.6 + - - +
128D ALA* 3.4 0.9 + - - -
129D THR* 2.8 35.2 + - + +
133D MET* 3.6 21.3 - - + -
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 6.3 0.2 - - - -
122D TYR* 3.0 20.6 + - + +
123D ASP* 3.8 4.0 - - - +
125D ILE* 1.3 75.3 - - - +
127D GLU* 1.3 59.1 + - - +
129D THR* 3.9 4.5 - - - -
130D GLY* 2.9 30.1 + - - -
131D ASN 4.0 6.7 - - - +
133D MET* 3.6 28.3 - - + -
157D ASN* 3.5 30.7 - - + +
159D LYS* 3.7 32.3 - - + -
160D VAL* 3.6 31.0 - - + +
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASP 2.9 19.1 + - - +
124D SER* 3.9 5.4 - - - +
126D ILE* 1.3 78.0 - - - +
128D ALA* 1.3 63.1 + - - +
129D THR 3.4 0.5 + - - -
130D GLY* 4.1 4.0 + - - -
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 3.5 34.8 - - + -
93D LYS* 3.1 30.1 + - - +
124D SER 3.0 17.6 + - - +
125D ILE 4.0 2.7 - - - +
127D GLU* 1.3 77.3 - - - +
129D THR* 1.3 60.2 + - + +
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Residues in contact with THR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE 4.2 3.6 - - - +
92D GLY* 3.5 33.9 - - - -
93D LYS* 3.5 13.7 - - + +
96D THR* 3.6 30.8 - - - +
103D LEU* 3.6 13.0 - - + +
125D ILE* 2.8 26.8 + - + +
126D ILE* 3.5 3.1 + - - -
128D ALA* 1.3 82.6 - - + +
130D GLY* 1.3 60.6 + - - +
131D ASN* 3.1 14.0 + - - +
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Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D THR* 5.4 0.7 - - - -
126D ILE 2.9 14.5 + - - -
127D GLU 4.1 3.6 + - - -
128D ALA 3.8 1.0 - - - -
129D THR* 1.3 75.6 - - - +
131D ASN* 1.3 60.5 + - - +
132D TYR* 4.2 0.3 + - - -
159D LYS* 3.1 31.4 + - - +
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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