Contacts of the helix formed by residues 122 - 133 (chain D) in PDB entry 2IBS
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 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D VAL* 1.3 81.0 - - - +
123D LYS* 1.3 66.5 + - - +
124D ALA* 4.1 8.3 - - + +
125D VAL* 3.0 31.4 + - + +
126D LYS* 3.2 9.9 + - - +
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Residues in contact with LYS 123 (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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121D VAL 3.8 1.4 + - - -
122D PHE* 1.3 73.4 - - - +
124D ALA* 1.3 56.1 + - - +
126D LYS* 3.2 12.7 + - + +
127D ASP* 2.9 56.1 + - - +
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Residues in contact with ALA 124 (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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122D PHE* 3.2 7.7 - - + +
123D LYS* 1.3 79.1 - - - +
125D VAL* 1.3 58.5 + - + +
127D ASP* 3.6 12.2 - - - +
128D LEU* 3.2 31.5 + - + +
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Residues in contact with VAL 125 (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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89D ASP* 4.8 3.6 - - - +
92D LEU* 4.9 7.6 - - + -
121D VAL* 4.1 17.9 - - + -
122D PHE* 3.0 32.4 + - + +
124D ALA* 1.3 77.2 - - + +
126D LYS* 1.3 64.2 + - - +
128D LEU* 3.2 14.8 + - + +
129D TYR* 3.1 48.3 + - + +
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Residues in contact with LYS 126 (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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111D VAL* 3.2 40.6 + - + -
112D GLY* 5.1 1.0 - - - -
121D VAL* 4.2 8.7 - - + +
122D PHE 3.2 11.0 + - - +
123D LYS* 3.2 14.6 + - + +
125D VAL* 1.3 76.0 - - - +
127D ASP* 1.3 58.1 + - - +
129D TYR* 3.2 12.5 + - + +
130D LYS* 3.0 39.4 + - - +
136D TRP* 4.1 27.6 - - + +
139D LYS* 4.9 5.8 + - - +
19F A 3.2 17.6 + - - -
20F C 2.9 28.7 + - - +
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Residues in contact with ASP 127 (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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123D LYS* 2.9 46.1 + - - +
124D ALA* 3.6 13.2 - - - +
125D VAL 3.2 0.2 - - - -
126D LYS* 1.3 78.9 - - - +
128D LEU* 1.3 58.1 + - - +
130D LYS* 3.5 19.5 + - - +
131D LYS* 3.1 27.1 + - - +
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Residues in contact with LEU 128 (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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92D LEU* 3.9 35.5 - - + +
124D ALA* 3.2 20.2 + - + +
125D VAL* 3.2 17.7 + - + +
127D ASP* 1.3 74.3 - - - +
129D TYR* 1.3 61.2 + - - +
131D LYS* 3.7 18.7 - - + +
132D ALA* 3.1 29.6 + - - +
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Residues in contact with TYR 129 (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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89D ASP* 2.6 32.1 + - - -
91D LEU* 3.7 38.9 - - + +
92D LEU* 4.0 18.2 - - + -
111D VAL* 4.9 4.5 - - + -
119D ILE* 6.2 0.4 - - + -
121D VAL* 4.7 15.6 - - + +
125D VAL* 3.1 32.1 + - + +
126D LYS* 3.2 14.1 + - - +
128D LEU* 1.3 76.8 - - - +
130D LYS* 1.3 56.7 + - - +
132D ALA* 3.4 0.6 + - - -
133D PHE* 3.0 42.8 + + + +
136D TRP* 3.7 32.1 - + + -
142D LEU* 4.4 12.2 - - + +
1002D NEA 4.5 3.6 + - - -
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Residues in contact with LYS 130 (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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126D LYS* 3.0 31.7 + - - +
127D ASP* 3.8 18.6 + - - +
128D LEU 3.4 0.2 - - - -
129D TYR* 1.3 73.3 - - - +
131D LYS* 1.3 64.8 + - - +
133D PHE 3.3 16.3 - - - +
136D TRP* 3.9 41.0 - - + +
20F C 2.7 37.8 + - - -
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Residues in contact with LYS 131 (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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127D ASP 3.1 17.5 + - - +
128D LEU* 3.7 22.2 - - + +
130D LYS* 1.3 79.1 - - - +
132D ALA* 1.3 60.8 + - - +
133D PHE 3.7 0.7 + - - -
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Residues in contact with ALA 132 (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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91D LEU 4.6 7.9 - - - +
92D LEU* 4.6 7.0 - - + -
128D LEU 3.1 17.6 + - - +
129D TYR 3.4 3.6 + - - +
130D LYS 3.3 0.2 - - - -
131D LYS* 1.3 78.2 - - + +
133D PHE* 1.3 81.5 + - + +
134D SER 4.0 1.1 + - - -
148D GLU* 3.9 5.4 - - - +
152D ARG* 4.6 8.5 + - - -
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Residues in contact with PHE 133 (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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91D LEU* 3.4 52.7 - - + -
129D TYR* 3.0 34.8 + + - +
130D LYS 3.3 14.0 - - - +
131D LYS 3.5 1.5 - - - -
132D ALA* 1.3 87.9 - - + +
134D SER* 1.3 63.7 + - - +
135D THR* 3.2 1.8 + - - +
136D TRP* 3.4 26.9 + + + +
140D TYR* 5.5 0.2 - - + -
145D ALA* 3.5 39.0 - - + -
148D GLU* 3.2 24.9 - - - +
149D LYS* 3.6 22.9 - - + -
152D ARG* 5.4 2.5 - - - -
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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