Contacts of the helix formed by residues 102 - 114 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.9 8.0 - - - +
100A ARG* 3.9 24.9 - - + +
101A TRP* 1.3 85.9 + - - +
103A PRO* 1.3 74.9 - - - +
104A ASP* 3.1 25.1 + - - +
105A ASP* 3.1 22.3 + - - +
106A GLU* 3.1 19.8 + - - +
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Residues in contact with PRO 103 (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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102A THR* 1.3 88.8 - - - +
104A ASP* 1.3 57.8 + - - +
106A GLU* 3.3 10.2 + - + +
107A MET* 2.8 40.2 + - + +
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Residues in contact with ASP 104 (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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16A ARG* 3.8 26.0 - - + -
17A PRO* 5.7 2.0 - - + -
102A THR* 3.1 11.8 + - - +
103A PRO* 1.3 77.8 - - - +
105A ASP* 1.3 68.3 + - - +
107A MET* 3.2 28.4 + - + +
108A VAL* 3.2 24.8 + - - +
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Residues in contact with ASP 105 (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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16A ARG* 2.7 43.8 + - - +
19A VAL* 4.7 0.5 - - - +
94A PHE* 3.5 10.8 - - - -
95A VAL 4.6 1.2 - - - +
96A VAL* 3.4 29.2 - - + +
97A GLU 4.9 0.3 + - - -
100A ARG 4.6 2.9 - - - +
101A TRP* 3.8 30.7 - - + -
102A THR* 3.1 30.6 + - - +
104A ASP* 1.3 80.3 - - - +
106A GLU* 1.3 61.3 + - - +
108A VAL* 3.2 7.4 + - - +
109A LEU* 3.0 17.0 + - - +
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Residues in contact with GLU 106 (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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101A TRP* 4.0 27.8 + - + +
102A THR 3.1 12.4 + - - +
103A PRO* 3.6 11.7 - - + +
104A ASP 3.1 0.2 - - - -
105A ASP* 1.3 73.9 - - - +
107A MET* 1.3 59.7 + - - +
109A LEU* 3.0 8.6 + - + +
110A ASN* 2.8 48.7 + - - +
145A GLN* 4.8 6.7 - - - +
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Residues in contact with MET 107 (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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103A PRO* 2.8 20.2 + - + +
104A ASP* 3.2 33.1 + - + +
106A GLU* 1.3 73.6 - - - +
108A VAL* 1.3 58.9 + - + +
110A ASN* 3.5 17.4 - - - +
111A LYS* 3.1 36.1 - - - +
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Residues in contact with VAL 108 (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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14A VAL* 4.2 13.0 - - + -
15A GLY 3.8 15.7 - - - +
16A ARG* 3.9 23.6 - - + +
94A PHE* 3.5 26.9 - - + -
104A ASP 3.2 13.3 + - - +
105A ASP 3.4 7.4 - - - +
106A GLU 3.1 0.4 - - - -
107A MET* 1.3 76.3 - - + +
109A LEU* 1.3 64.2 + - - +
111A LYS* 3.1 17.0 + - - +
112A LEU* 3.4 13.5 - - + +
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Residues in contact with LEU 109 (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 PHE* 4.1 21.7 - - + -
101A TRP* 4.4 9.9 - - + -
105A ASP 3.0 11.7 + - - +
106A GLU* 3.0 15.8 + - + +
108A VAL* 1.3 75.7 - - - +
110A ASN* 1.3 56.8 + - - +
111A LYS 3.0 0.2 - - - -
112A LEU* 2.8 34.7 + - + +
113A ARG* 3.0 31.1 + - - +
145A GLN* 3.9 32.3 - - + +
146A MET* 3.5 33.2 - - + -
148A PHE* 4.4 4.5 - - + -
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Residues in contact with ASN 110 (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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106A GLU* 2.8 38.0 + - - +
107A MET* 3.5 21.7 - - - +
108A VAL 3.2 0.2 - - - -
109A LEU* 1.3 76.1 - - - +
111A LYS* 1.3 60.7 + - + +
112A LEU 3.3 0.2 - - - -
113A ARG* 3.2 36.2 + - - +
114A GLU* 3.6 15.0 - - - +
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Residues in contact with LYS 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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64A PRO* 4.3 21.1 - - + +
107A MET* 3.1 31.9 - - - +
108A VAL* 3.1 8.7 + - - +
109A LEU 3.0 1.2 - - - -
110A ASN* 1.3 78.8 - - + +
112A LEU* 1.3 67.4 + - + +
114A GLU* 3.6 29.9 - - - +
115A GLY* 4.3 3.5 + - - -
304A SO4 4.6 17.7 + - - +
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Residues in contact with LEU 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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14A VAL* 4.3 9.2 - - + -
64A PRO* 4.0 21.3 - - + -
92A VAL* 4.0 13.9 - - + -
94A PHE* 3.7 29.2 - - + -
108A VAL* 3.4 20.9 - - + +
109A LEU* 2.8 16.5 + - + +
111A LYS* 1.3 84.5 - - + +
113A ARG* 1.3 64.7 + - - +
114A GLU 3.1 0.9 - - - -
115A GLY* 3.1 18.8 + - - +
117A ALA 4.6 3.5 - - - +
119A VAL* 3.6 46.8 - - + +
146A MET* 4.4 5.0 - - - +
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Residues in contact with ARG 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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109A LEU* 3.0 38.7 + - - +
110A ASN* 3.2 37.7 + - - +
112A LEU* 1.3 69.8 - - - +
114A GLU* 1.3 53.2 + - + +
115A GLY 2.8 22.7 + - - +
145A GLN* 2.6 26.3 + - - -
146A MET* 3.5 20.6 - - - +
305A SO4 3.7 23.6 + - - +
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Residues in contact with GLU 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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110A ASN 3.6 14.3 - - - +
111A LYS* 3.6 29.2 - - - +
113A ARG* 1.3 79.9 - - + +
115A GLY* 1.3 54.8 + - - +
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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