Contacts of the helix formed by residues 102 - 114 (chain D) in PDB entry 2IHC
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 ASN 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D LYS* 3.9 21.1 - - + +
86D PRO* 4.1 12.5 - - - +
97D ILE* 3.6 19.6 + - - +
98D LEU* 3.5 5.4 - - - -
99D SER* 2.9 36.6 + - - +
101D GLU* 1.3 75.9 - - + +
103D VAL* 1.3 59.8 + - - -
104D ASP 3.4 2.7 - - - -
105D GLU* 3.3 8.8 + - - +
106D VAL* 2.9 44.3 + - - +
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Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 3.8 9.4 - - + -
99D SER 2.5 48.2 + - - +
100D LYS* 3.9 5.5 + - - +
101D GLU 3.6 2.0 - - - -
102D ASN* 1.3 77.8 - - - +
104D ASP* 1.3 64.3 + - - +
106D VAL* 4.0 3.7 - - - +
107D CYS* 3.0 27.1 + - + +
123D PHE* 3.6 47.5 - - + +
126D LEU* 3.7 18.2 - - + -
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Residues in contact with ASP 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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100D LYS 4.9 5.7 + - - +
101D GLU 5.2 1.7 + - - +
102D ASN 3.4 0.4 - - - -
103D VAL* 1.3 82.0 + - - +
105D GLU* 1.3 61.6 + - - +
107D CYS* 3.8 5.3 - - - +
108D LYS* 3.0 30.0 + - - +
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Residues in contact with GLU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D THR* 4.0 14.3 + - - +
82D LYS* 4.4 8.1 - - + -
83D GLY* 3.6 20.3 - - - +
101D GLU 5.5 1.5 + - - +
102D ASN* 3.3 12.0 + - - +
104D ASP* 1.3 77.3 - - - +
106D VAL* 1.3 58.7 + - - +
108D LYS* 3.7 4.2 + - - +
109D CYS* 3.1 29.1 + - - +
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Residues in contact with VAL 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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82D LYS 4.0 12.3 - - - +
83D GLY 3.8 8.7 - - - +
86D PRO* 4.0 10.5 - - + -
87D LEU* 3.6 24.0 - - + +
96D LEU* 4.0 11.0 - - + -
98D LEU* 3.8 24.0 - - + -
102D ASN* 2.9 43.2 + - - +
103D VAL 4.0 3.1 - - - +
105D GLU* 1.3 73.2 - - - +
107D CYS* 1.3 67.4 + - - +
109D CYS 3.2 0.7 + - - -
110D VAL* 2.9 32.9 + - + +
123D PHE* 4.9 1.6 - - + -
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Residues in contact with CYS 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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103D VAL* 3.0 21.2 + - + +
104D ASP* 3.8 7.2 - - - +
105D GLU 3.4 0.2 - - - -
106D VAL* 1.3 76.7 - - - +
108D LYS* 1.3 63.1 + - - +
110D VAL* 3.3 11.1 + - - +
111D GLU* 3.2 19.8 + - - +
123D PHE* 4.2 32.7 - - + -
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Residues in contact with LYS 108 (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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78D GLU 5.7 5.2 - - - +
104D ASP 3.0 18.6 + - - +
105D GLU* 4.0 5.2 - - - +
107D CYS* 1.3 77.3 - - - +
109D CYS* 1.3 58.1 + - - +
111D GLU* 3.1 9.0 + - - +
112D PHE* 2.9 28.2 + - - +
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Residues in contact with CYS 109 (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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78D GLU 5.6 3.1 + - - +
79D VAL* 3.9 29.2 - - + -
80D THR 5.6 0.9 - - - +
83D GLY* 4.1 8.7 - - - +
84D PHE* 4.0 12.6 - - - -
87D LEU* 3.8 12.1 - - - +
105D GLU 3.1 19.3 + - - +
106D VAL 3.2 4.0 + - - +
108D LYS* 1.3 76.9 - - - +
110D VAL* 1.3 56.8 + - - +
112D PHE* 4.3 6.3 - - - -
113D LEU* 2.9 52.3 + - - +
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Residues in contact with VAL 110 (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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87D LEU* 3.3 24.0 - - + -
106D VAL* 2.9 31.4 + - + +
107D CYS* 3.4 10.8 - - - +
109D CYS* 1.3 75.6 - - - +
111D GLU* 1.3 59.7 + - - +
114D SER* 2.9 28.4 + - - -
115D VAL* 3.1 32.2 + - + +
118D ILE* 4.2 15.9 - - + +
123D PHE* 4.6 12.6 - - + -
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Residues in contact with GLU 111 (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 CYS* 3.2 8.6 + - - +
108D LYS* 3.1 12.5 + - - +
110D VAL* 1.3 81.9 - - - +
112D PHE* 1.3 62.8 + - - +
114D SER* 3.6 13.1 + - - +
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Residues in contact with PHE 112 (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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58D TYR* 3.4 46.6 - + - +
75D LEU* 5.2 0.2 - - + -
76D PRO* 3.6 30.3 - - + -
78D GLU* 5.2 14.1 - - + -
79D VAL* 3.1 35.4 - - + -
108D LYS 2.9 15.6 + - - +
109D CYS* 4.0 5.8 - - - +
111D GLU* 1.3 79.0 - - - +
113D LEU* 1.3 70.2 + - + +
114D SER* 3.4 2.8 + - - -
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Residues in contact with LEU 113 (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 SER* 2.3 32.8 + - - +
58D TYR* 3.2 40.9 + - + +
59D PHE* 3.5 30.5 - - + -
79D VAL* 4.8 4.5 - - + -
84D PHE* 3.6 27.1 - - + -
87D LEU* 5.5 5.4 - - + -
109D CYS* 2.9 32.1 + - - +
112D PHE* 1.3 87.8 - - + +
114D SER* 1.3 64.1 + - - +
115D VAL* 4.5 9.4 - - + +
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Residues in contact with SER 114 (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 SER* 3.5 1.6 - - - -
57D SER* 3.3 36.0 + - - -
58D TYR 4.5 1.1 - - - -
110D VAL 2.9 12.1 + - - -
111D GLU* 3.6 11.4 + - - +
112D PHE 3.2 4.5 + - - -
113D LEU* 1.3 80.3 - - - +
115D VAL* 1.3 63.7 + - - +
116D HIS* 3.6 9.8 + - - -
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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