Contacts of the helix formed by residues 119 - 133 (chain B) in PDB entry 2IHB
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 PHE 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B PHE* 4.8 4.3 - + + -
66B CYS* 3.9 24.0 - - + -
69B PHE* 3.5 39.9 - + + -
82B ALA* 4.0 18.2 - - - -
85B ILE* 3.7 29.4 - - + -
86B TYR* 5.4 2.5 - + + -
90B LEU* 4.0 27.8 - - + -
116B PRO 4.8 0.4 + - - -
117B LEU 3.2 1.0 - - - -
118B MET* 1.3 109.7 - - + +
120B GLN* 1.3 64.0 + - - +
121B LYS* 3.5 2.2 - - - -
122B LEU* 3.2 15.0 + - + -
123B GLN* 2.8 22.3 + - - +
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Residues in contact with GLN 120 (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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70B LYS* 2.9 37.1 + - - +
117B LEU* 3.2 38.6 + - + +
118B MET 3.4 1.4 - - - -
119B PHE* 1.3 75.6 - - - +
121B LYS* 1.3 65.7 + - - +
123B GLN* 3.1 8.1 + - - +
124B ASP* 2.8 63.2 + - - +
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Residues in contact with LYS 121 (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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118B MET 5.3 1.0 + - - +
120B GLN* 1.3 76.6 - - - +
122B LEU* 1.3 63.5 + - + +
124B ASP* 3.5 7.1 + - - +
125B GLN* 3.0 48.5 + - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.0 14.1 - - + -
90B LEU* 3.9 31.9 - - + -
100B VAL* 3.2 37.4 - - + +
101B GLU 5.8 1.6 - - - +
118B MET 5.6 1.3 - - - +
119B PHE* 3.2 21.0 + - + +
121B LYS* 1.3 77.9 - - + +
123B GLN* 1.3 66.3 + - - +
125B GLN* 3.2 11.3 + - - +
126B ILE* 3.1 26.7 + - - +
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Residues in contact with GLN 123 (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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62B PHE* 4.0 10.8 - - - -
63B TRP* 3.3 41.6 + - + +
66B CYS* 3.6 22.9 - - + +
67B GLU* 2.7 33.3 + - - +
70B LYS* 2.8 29.3 + - - +
119B PHE 2.8 20.6 + - - +
120B GLN* 3.2 13.0 - - - +
122B LEU* 1.3 72.6 - - - +
124B ASP* 1.3 59.7 + - - +
126B ILE* 3.4 1.8 + - - +
127B PHE* 2.9 28.3 + - - +
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Residues in contact with ASP 124 (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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120B GLN* 2.8 49.6 + - - +
121B LYS* 3.7 7.0 + - - +
123B GLN* 1.3 75.1 - - - +
125B GLN* 1.3 56.4 + - + +
127B PHE* 3.3 9.6 + - - +
128B ASN* 2.9 41.2 + - - +
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Residues in contact with GLN 125 (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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180A LYS* 6.1 1.3 - - - +
99B ASN 5.8 0.4 - - - +
100B VAL* 2.7 36.8 - - + +
101B GLU* 3.1 49.1 + - + +
121B LYS* 3.0 37.9 + - - +
122B LEU* 3.2 12.7 + - - +
124B ASP* 1.3 76.4 - - - +
126B ILE* 1.3 59.8 + - + +
128B ASN* 3.3 9.5 + - - +
129B LEU* 3.0 26.3 + - - +
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Residues in contact with ILE 126 (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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59B ASN* 3.4 50.5 - - + +
62B PHE* 3.6 24.9 - - + -
63B TRP* 5.0 2.5 - - + -
98B VAL* 4.0 17.9 - - + -
99B ASN 3.6 32.3 - - - +
100B VAL* 4.4 6.5 - - + -
122B LEU 3.1 15.1 + - - +
123B GLN 4.0 3.1 - - - +
125B GLN* 1.3 74.6 - - - +
127B PHE* 1.3 65.2 + - - +
129B LEU* 3.5 6.3 - - + +
130B MET* 3.1 27.3 + - + +
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Residues in contact with PHE 127 (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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34B LEU* 3.6 34.5 - - + +
35B GLU* 3.6 41.3 - - + -
38B LEU* 3.9 12.3 - - + -
63B TRP* 3.7 25.6 - + - +
123B GLN 2.9 15.6 + - - +
124B ASP* 3.3 14.1 - - - +
126B ILE* 1.3 78.8 - - - +
128B ASN* 1.3 69.6 + - - +
130B MET* 3.5 8.6 + - - +
131B LYS* 2.9 47.4 + - + +
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Residues in contact with ASN 128 (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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115A GLU* 5.7 0.7 - - - +
124B ASP* 2.9 28.3 + - - +
125B GLN* 3.3 6.3 + - - +
127B PHE* 1.3 88.3 - - - +
129B LEU* 1.3 64.3 + - - +
131B LYS* 4.1 9.5 + - - +
132B TYR* 3.3 46.4 + - + +
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Residues in contact with LEU 129 (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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179A VAL* 5.5 0.2 - - - +
180A LYS* 3.6 54.5 - - + +
182A THR* 3.9 26.9 - - + +
59B ASN* 3.8 23.6 - - - +
99B ASN* 3.7 27.6 - - + +
125B GLN 3.0 13.5 + - - +
126B ILE* 3.5 12.3 - - + +
128B ASN* 1.3 77.4 - - - +
130B MET* 1.3 62.4 + - + +
132B TYR* 4.3 0.5 - - - +
133B ASP* 3.1 29.1 + - - +
134B SER* 5.0 0.7 - - - -
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Residues in contact with MET 130 (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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182A THR* 5.5 0.2 - - - -
34B LEU* 3.8 7.6 - - + -
38B LEU* 4.4 14.4 - - + -
47B PHE* 4.1 24.5 - - + -
51B LEU* 4.8 1.8 - - + -
59B ASN* 3.8 17.7 - - + +
60B VAL* 3.8 28.9 - - - -
63B TRP* 4.1 26.7 - - + -
126B ILE* 3.1 23.9 + - + +
127B PHE* 3.7 15.0 - - - +
129B LEU* 1.3 77.6 - - - +
131B LYS* 1.3 64.9 + - - +
132B TYR 3.3 0.7 + - - -
133B ASP 3.3 4.9 + - - -
134B SER* 3.3 17.0 + - - +
135B TYR* 3.0 25.4 + - - +
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Residues in contact with LYS 131 (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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71A VAL* 6.0 2.0 - - - -
115A GLU* 3.3 38.0 + - - +
34B LEU* 3.8 18.4 - - + +
35B GLU* 5.2 8.4 + - - +
127B PHE* 2.9 39.6 + - + +
128B ASN* 3.9 11.6 + - - +
129B LEU 3.4 0.6 - - - -
130B MET* 1.3 78.8 - - - +
132B TYR* 1.3 95.4 + - + +
133B ASP 3.6 0.2 + - - -
135B TYR* 3.5 26.3 - - + +
136B SER* 3.9 4.9 + - - -
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Residues in contact with TYR 132 (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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71A VAL* 4.5 21.4 - - + +
72A VAL* 4.1 29.9 - - + +
75A SER* 3.7 32.1 + - - -
115A GLU* 3.3 22.5 + - - -
179A VAL* 3.4 29.9 - - + +
128B ASN* 3.3 39.5 + - + +
129B LEU 4.8 0.4 - - - +
131B LYS* 1.3 105.2 - - + +
133B ASP* 1.3 58.4 + - - +
136B SER* 3.8 13.4 + - - -
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Residues in contact with ASP 133 (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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179A VAL* 3.9 11.0 - - + +
180A LYS 3.4 22.2 - - - +
181A THR* 3.8 8.9 + - - +
182A THR* 3.1 30.7 + - + +
129B LEU 3.1 17.9 + - - +
130B MET 3.3 1.0 + - - -
132B TYR* 1.3 79.1 - - - +
134B SER* 1.3 64.4 + - - +
135B TYR 3.5 0.9 - - - -
136B SER* 3.3 13.1 + - - -
137B ARG* 2.7 47.6 + - - +
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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