Contacts of the helix formed by residues 102 - 114 (chain B) in PDB entry 3IEU
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ARG* 3.9 7.6 - - - +
100B ARG* 3.9 25.1 - - + +
101B TRP* 1.3 84.0 + - - +
103B PRO* 1.4 77.3 - - - +
104B ASP* 3.1 24.2 + - - +
105B ASP* 3.1 22.9 + - - +
106B GLU* 3.1 18.6 + - - +
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Residues in contact with PRO 103 (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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102B THR* 1.4 89.2 - - - +
104B ASP* 1.3 57.4 + - - +
106B GLU* 3.3 10.0 + - + +
107B MET* 2.8 39.9 + - + +
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Residues in contact with ASP 104 (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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16B ARG* 3.7 26.3 - - + -
17B PRO* 6.0 1.6 - - - -
102B THR* 3.1 11.3 + - - +
103B PRO* 1.3 76.7 - - - +
105B ASP* 1.3 66.1 + - - +
107B MET* 3.1 36.2 + - + +
108B VAL* 3.2 18.0 + - - +
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Residues in contact with ASP 105 (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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16B ARG* 2.8 42.4 + - - +
19B VAL* 4.7 0.2 - - - +
94B PHE* 3.5 10.5 - - - -
95B VAL 4.6 1.6 - - - +
96B VAL* 3.3 29.9 - - + +
97B GLU 4.9 0.2 + - - -
100B ARG 4.4 3.0 - - - +
101B TRP* 3.8 28.8 - - + -
102B THR* 3.1 29.5 + - - +
104B ASP* 1.3 79.0 - - - +
106B GLU* 1.3 62.1 + - - +
108B VAL* 3.2 7.8 + - - +
109B LEU* 3.0 17.7 + - - +
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Residues in contact with GLU 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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101B TRP* 4.0 27.9 + - + +
102B THR 3.1 11.6 + - - +
103B PRO* 3.6 12.3 - - + +
104B ASP 3.1 0.2 - - - -
105B ASP* 1.3 75.4 - - - +
107B MET* 1.3 60.6 + - - +
109B LEU* 3.0 8.7 + - + +
110B ASN* 2.8 49.4 + - - +
145B GLN* 5.0 6.5 - - - +
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Residues in contact with MET 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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103B PRO* 2.8 21.3 + - + +
104B ASP* 3.1 33.0 + - + +
106B GLU* 1.3 72.6 - - - +
108B VAL* 1.3 59.2 + - + +
110B ASN* 3.5 17.6 - - - +
111B LYS* 3.1 36.8 - - - +
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Residues in contact with VAL 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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14B VAL* 4.2 11.9 - - + -
15B GLY* 3.8 13.5 - - - +
16B ARG* 3.9 24.2 - - + +
94B PHE* 3.4 29.8 - - + -
104B ASP 3.2 13.7 + - - +
105B ASP 3.3 7.6 - - - +
106B GLU 3.1 0.4 - - - -
107B MET* 1.3 74.1 - - + +
109B LEU* 1.3 66.5 + - - +
111B LYS* 3.1 16.8 + - - +
112B LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 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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94B PHE* 4.1 22.2 - - + -
101B TRP* 4.4 10.5 - - + -
105B ASP 3.0 12.3 + - - +
106B GLU* 3.0 14.9 + - + +
108B VAL* 1.3 75.5 - - - +
110B ASN* 1.3 56.0 + - - +
112B LEU* 2.8 34.0 + - + +
113B ARG* 3.0 32.9 + - - +
145B GLN* 3.9 32.3 - - + +
146B MET* 3.4 34.1 - - + -
148B PHE* 4.4 4.5 - - + -
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Residues in contact with ASN 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 GLU* 2.8 42.3 + - - +
107B MET* 3.5 21.9 - - - +
109B LEU* 1.3 71.5 - - - +
111B LYS* 1.3 61.5 + - + +
112B LEU 3.3 0.4 - - - -
113B ARG* 3.2 36.0 + - - +
114B GLU* 3.6 15.3 - - - +
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Residues in contact with LYS 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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64B PRO* 4.4 19.3 - - + +
107B MET* 3.1 31.0 - - - +
108B VAL* 3.1 7.8 + - - +
109B LEU 2.9 1.4 + - - -
110B ASN* 1.3 79.8 - - + +
112B LEU* 1.3 68.4 + - + +
113B ARG 3.6 0.2 - - - -
114B GLU* 3.6 31.0 - - - +
115B GLY* 4.2 3.5 + - - -
304B SO4 4.8 14.6 + - - +
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Residues in contact with LEU 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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14B VAL* 4.3 9.2 - - + -
64B PRO* 4.1 21.5 - - + -
92B VAL* 4.0 13.9 - - + -
94B PHE* 3.8 28.3 - - + -
108B VAL* 3.4 22.0 - - + +
109B LEU* 2.8 16.9 + - + +
111B LYS* 1.3 85.9 - - + +
113B ARG* 1.3 65.7 + - - +
114B GLU 3.1 0.9 - - - -
115B GLY* 3.1 17.9 + - - +
117B ALA 4.6 3.3 - - - +
119B VAL* 3.6 46.2 - - + +
146B MET* 4.3 4.2 - - - +
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Residues in contact with ARG 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 LEU* 3.0 38.2 + - - +
110B ASN* 3.2 38.7 + - - +
112B LEU* 1.3 70.4 - - - +
114B GLU* 1.3 53.0 + - - +
115B GLY 2.8 23.6 + - - +
145B GLN* 2.6 27.1 + - - -
146B MET* 3.5 24.6 - - + +
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Residues in contact with GLU 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 ASN 3.6 14.6 + - - +
111B LYS* 3.6 29.6 - - - +
113B ARG* 1.3 78.8 - - + +
115B GLY* 1.3 55.0 + - - -
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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