Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 4BEJ
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 ASP 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A TYR* 4.4 1.3 - - - +
102A THR* 1.3 82.4 - - + +
104A PHE* 1.3 58.4 + - - +
105A ASP* 3.0 26.4 + - - +
106A GLU* 3.0 44.9 + - + +
107A ILE* 3.3 10.6 + - - +
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Residues in contact with PHE 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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46A VAL* 4.9 0.7 - - + -
48A ARG* 3.2 57.9 - - + +
49A ASP 4.7 7.2 - - - +
50A LEU* 4.1 28.1 - - + -
89A GLU* 3.8 29.4 - - + -
90A TRP* 4.2 8.5 - - - -
102A THR 4.4 7.9 - - - -
103A ASP* 1.3 71.2 + - - +
105A ASP* 1.3 64.0 + - - +
106A GLU 3.1 1.6 - - - -
107A ILE* 3.3 30.6 + - + +
108A ARG* 3.2 22.7 + - - +
134A ILE* 3.9 37.2 - - + -
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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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49A ASP 6.0 0.2 - - - -
103A ASP* 3.0 18.0 + - - +
104A PHE* 1.3 77.9 - - - +
106A GLU* 1.3 57.7 + - - +
108A ARG* 2.4 46.1 + - - +
109A GLN* 3.1 24.6 + - - +
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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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99A LYS* 4.0 14.7 - - - -
101A TYR* 2.9 34.4 - - + +
102A THR* 5.4 0.5 + - - +
103A ASP* 3.0 32.6 + - + +
105A ASP* 1.3 79.7 - - - +
107A ILE* 1.3 58.8 + - - +
109A GLN* 3.7 6.5 - - + +
110A GLU* 2.9 32.4 + - + +
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Residues in contact with ILE 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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50A LEU* 4.6 10.5 - - + -
91A GLY* 4.2 16.4 - - - +
93A PHE* 3.4 15.7 - - + -
101A TYR* 3.7 27.8 - - + +
103A ASP 3.6 11.0 - - - +
104A PHE* 3.3 43.3 + - + +
106A GLU* 1.3 77.1 - - - +
108A ARG* 1.3 62.9 + - - +
110A GLU 3.2 1.0 + - - -
111A ILE* 3.1 27.0 + - + +
132A LEU* 3.5 32.3 - - + -
134A ILE* 4.8 4.0 - - + -
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Residues in contact with ARG 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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49A ASP* 4.3 15.9 + - - -
50A LEU* 3.3 24.9 + - - +
51A LEU 4.2 12.1 - - - -
52A PRO* 4.0 13.0 - - + +
53A ARG* 5.4 4.9 - - - +
104A PHE 3.2 11.6 + - - +
105A ASP* 2.4 47.3 + - - +
107A ILE* 1.3 80.4 - - - +
109A GLN* 1.3 76.5 + - - +
111A ILE* 3.3 7.0 + - - +
112A GLU* 3.2 41.7 + - - +
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Residues in contact with GLN 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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105A ASP 3.1 16.5 + - - +
106A GLU* 3.7 9.4 - - + +
107A ILE 3.3 0.2 - - - -
108A ARG* 1.3 91.6 + - - +
110A GLU* 1.3 56.5 + - - +
112A GLU* 3.5 25.2 + - - +
113A ASN* 3.0 64.8 + - - +
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Residues in contact with GLU 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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93A PHE* 3.8 23.3 - - + -
95A HIS* 2.8 34.6 + - + +
96A THR* 4.2 4.3 - - - +
101A TYR* 4.0 17.3 + - + +
106A GLU* 2.9 18.0 + - + +
107A ILE 3.5 5.4 - - - +
108A ARG 3.2 0.2 - - - -
109A GLN* 1.3 74.5 - - - +
111A ILE* 1.3 56.1 + - - +
113A ASN* 3.4 15.2 + - - +
114A GLU* 2.8 36.8 + - - +
117A ARG* 4.3 14.0 + - - -
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Residues in contact with ILE 111 (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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50A LEU* 3.6 29.4 - - + +
51A LEU* 4.9 3.4 - - + -
52A PRO* 4.0 21.3 - - + -
59A THR* 4.6 8.7 - - + -
63A LEU* 4.9 17.7 - - + -
93A PHE* 4.1 13.9 - - + -
107A ILE* 3.1 13.9 + - + +
108A ARG 3.5 6.5 - - - +
110A GLU* 1.3 74.3 - - - +
112A GLU* 1.3 62.6 + - - +
114A GLU* 3.5 1.7 + - - +
115A THR* 2.9 35.2 + - - +
130A ILE* 4.4 18.2 - - + +
132A LEU* 4.0 21.1 - - + -
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Residues in contact with GLU 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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52A PRO* 3.3 36.1 - - + +
54A GLY* 5.4 4.7 + - - -
59A THR* 6.2 1.1 - - - -
108A ARG* 3.2 31.7 + - - +
109A GLN* 3.5 30.2 + - - +
110A GLU 3.3 0.2 - - - -
111A ILE* 1.3 78.6 - - - +
113A ASN* 1.3 58.3 + - - +
115A THR* 3.4 7.0 + - - -
116A GLU* 3.1 30.0 + - - +
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Residues in contact with ASN 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 GLN* 3.0 49.6 + - - +
110A GLU* 3.4 18.5 + - - +
111A ILE 3.2 0.2 - - - -
112A GLU* 1.3 75.8 - - - +
114A GLU* 1.3 62.4 + - - +
116A GLU* 3.4 8.8 + - - +
117A ARG* 2.6 48.1 + - - +
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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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61A ARG* 2.2 54.3 + - - +
95A HIS* 4.2 31.0 + - + +
110A GLU* 2.8 20.4 + - - +
111A ILE 4.0 4.0 - - - +
112A GLU 3.5 0.2 - - - -
113A ASN* 1.3 73.6 - - - +
115A THR* 1.3 61.5 + - - +
117A ARG* 3.1 35.0 + - - +
118A ILE* 3.9 2.9 + - - +
128A GLU* 5.2 1.0 - - - +
130A ILE* 3.9 26.2 - - + -
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Residues in contact with THR 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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58A VAL 4.0 8.3 - - - +
59A THR* 4.0 19.9 - - + +
60A ARG* 3.4 49.5 + - + +
61A ARG* 4.7 15.2 + - - +
111A ILE* 2.9 17.4 + - - +
112A GLU* 3.5 10.3 - - - -
113A ASN 3.1 0.6 - - - -
114A GLU* 1.3 75.9 - - - +
116A GLU* 1.3 64.2 + - - +
118A ILE* 3.4 18.2 - - - +
130A ILE* 6.1 1.2 - - - +
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Residues in contact with GLU 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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60A ARG* 3.7 17.4 + - - +
112A GLU 3.1 15.1 + - - +
113A ASN* 3.9 8.3 - - - +
115A THR* 1.3 81.0 - - - +
117A ARG* 1.3 76.6 + - - +
118A ILE 3.3 4.9 + - - -
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Residues in contact with ARG 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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95A HIS* 6.3 0.4 - - - -
110A GLU* 4.3 11.0 + - - -
113A ASN* 2.6 58.6 + - - +
114A GLU* 3.1 31.0 + - - +
116A GLU* 1.3 85.5 + - - +
118A ILE* 1.3 63.5 + - + +
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Residues in contact with ILE 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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60A ARG* 5.0 17.9 - - + +
61A ARG* 3.5 43.1 - - + +
114A GLU* 3.9 1.5 + - - +
115A THR 3.4 16.3 + - - +
116A GLU 3.3 7.8 + - - -
117A ARG* 1.3 85.1 - - + +
125A VAL* 4.5 7.2 - - - +
126A SER* 3.7 31.4 - - - +
128A GLU* 4.8 8.3 - - - +
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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