Contacts of the helix formed by residues 100 - 107 (chain D) in PDB entry 4IL6
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 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D LEU* 3.9 1.3 - - - -
97D ALA* 3.2 16.6 + - - +
98D GLN 3.3 2.0 + - - +
99D GLY* 1.3 74.5 - - - +
101D PHE* 1.3 57.9 + - - +
102D THR* 3.1 21.5 + - - -
103D ARG* 3.1 29.1 + - + +
104D TRP* 3.0 28.4 + - - +
418D GOL 4.0 13.4 - - - +
419D HTG 3.9 11.7 + - - -
73E LYS* 3.7 20.7 + - - -
77E GLU* 4.7 1.0 - - - +
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Residues in contact with PHE 101 (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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50D THR* 5.7 1.1 - - + -
92D LEU* 3.8 19.1 - - + -
99D GLY 3.4 2.2 + - - +
100D ASP* 1.3 70.6 + - - +
102D THR* 1.3 67.0 + - - +
104D TRP* 3.4 29.9 - + - +
105D CYS* 3.1 43.4 + - - -
110D LEU* 5.6 1.1 - - + -
406D BCR 3.9 21.8 - + - -
418D GOL 3.3 18.1 + - - +
419D HTG 3.7 47.6 - - + -
46E VAL* 3.8 15.0 - - + -
47E PHE* 3.8 26.9 - + - -
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Residues in contact with THR 102 (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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100D ASP* 3.1 4.2 + - - -
101D PHE* 1.3 77.5 - - - +
103D ARG* 1.3 80.8 + - - +
105D CYS* 3.2 6.5 + - - +
106D GLN* 3.1 21.8 + - - +
419D HTG 2.9 34.5 + - - +
45E ASP 3.5 6.9 + - - +
46E VAL 2.7 20.3 + - - +
47E PHE 4.6 1.3 - - - -
48E GLY* 3.5 33.0 - - - +
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Residues in contact with ARG 103 (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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97D ALA* 4.8 2.0 - - - +
100D ASP* 3.1 31.3 + - + +
102D THR* 1.3 89.5 - - - +
104D TRP* 1.3 57.0 + - - +
106D GLN* 2.8 38.9 + - - +
107D LEU* 2.8 41.1 + - + +
419D HTG 5.7 0.6 + - - -
73E LYS* 3.7 36.2 + - + +
76E VAL* 4.1 10.9 - - - +
77E GLU* 3.3 37.2 + - - +
80E LEU* 3.5 27.9 - - - +
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Residues in contact with TRP 104 (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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90D LEU* 2.8 39.8 + - + -
91D LEU 4.1 0.2 - - - -
92D LEU* 3.4 32.2 - - + +
97D ALA* 3.7 14.7 - - + +
100D ASP 3.0 18.5 + - - +
101D PHE* 3.4 36.3 - + - +
103D ARG* 1.3 75.7 - - - +
105D CYS* 1.3 65.8 + - - +
107D LEU* 3.3 9.3 + - - +
109D GLY* 2.9 48.3 + - - -
110D LEU* 3.7 21.3 - - + -
113D PHE* 3.5 35.9 - + + -
405D CLA 3.7 22.4 - - + -
406D BCR 4.1 7.4 - + - -
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Residues in contact with CYS 105 (chain D).
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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55D VAL* 3.9 30.9 - - + +
56D THR 4.6 2.6 - - - +
101D PHE* 3.1 50.6 + - - -
102D THR 3.2 7.8 + - - +
104D TRP* 1.3 81.9 - - - +
106D GLN* 1.3 61.8 + - - +
108D GLY* 3.3 13.3 + - - -
109D GLY 4.8 2.0 - - - +
110D LEU* 4.4 14.3 + - - +
47E PHE* 3.6 26.5 - - - +
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Residues in contact with GLN 106 (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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56D THR* 5.1 8.5 - - + +
57D SER* 6.1 0.3 - - - -
59D TYR* 3.6 42.8 + - + +
60D THR* 3.5 17.2 + - - +
102D THR* 3.1 15.0 + - - +
103D ARG* 2.8 45.7 + - - +
105D CYS* 1.3 75.3 - - - +
107D LEU* 1.3 59.2 + - - +
108D GLY 3.4 0.2 - - - -
47E PHE 4.0 6.1 - - - +
48E GLY* 2.9 38.8 + - - +
76E VAL* 3.3 22.6 - - + +
80E LEU* 4.4 6.9 - - - +
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Residues in contact with LEU 107 (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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60D THR* 3.6 8.5 - - + +
81D PRO* 3.4 21.8 - - - +
82D ALA 4.3 1.2 + - - -
85D MET* 4.3 8.4 - - - +
90D LEU* 3.6 15.1 - - + +
96D GLU* 3.9 34.8 - - + +
97D ALA* 4.3 6.3 - - + +
103D ARG* 2.8 27.4 + - + +
104D TRP 3.3 4.7 + - - +
105D CYS 3.2 0.6 - - - -
106D GLN* 1.3 80.5 - - + +
108D GLY* 1.3 58.2 + - - +
66E VAL* 3.8 25.1 - - + -
72E ALA* 3.4 35.2 - - + +
73E LYS 4.5 4.7 - - - +
76E VAL* 4.6 4.7 - - + -
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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