Contacts of the helix formed by residues 121 - 136 (chain B) in PDB entry 2I91
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 ILE 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B CYS 4.4 0.7 - - - -
120B ARG* 1.3 84.1 - - - +
122B PRO* 1.3 76.6 - - + +
123B THR* 3.9 20.9 - - - +
124B HIS* 2.9 47.3 + - + +
125B LEU 3.5 2.1 + - - -
155B TRP* 4.0 5.5 - - - -
171B TYR* 4.0 17.0 - - + +
12F U 4.0 13.5 - - - +
13F C 3.8 37.0 - - - +
14F A 3.8 15.5 - - - +
15F A 4.0 6.1 - - - +
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG 4.7 0.2 - - - +
121B ILE* 1.3 87.1 - - + +
123B THR* 1.3 62.5 + - - +
125B LEU* 2.9 8.5 + - + +
126B PHE* 2.8 38.2 + - + -
155B TRP* 3.8 24.1 - - + -
159B LYS* 5.6 0.2 - - - +
167B ALA* 3.7 26.7 - - + +
171B TYR* 3.7 22.7 - - + -
179B HIS* 3.3 31.4 - - + +
15F A 5.8 0.9 - - - +
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 3.0 9.1 + - - -
122B PRO* 1.3 76.8 - - - +
124B HIS* 1.3 57.2 + - + +
126B PHE* 3.2 11.6 + - - +
127B THR* 2.8 42.9 + - - +
171B TYR* 3.4 18.5 - - - -
174B ARG* 3.5 17.6 - - + +
175B ASN* 4.3 13.5 - - - +
11F U 4.8 7.9 - - + -
12F U 2.7 28.8 + - - +
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Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN* 3.3 46.7 + - + +
93B LEU* 3.2 22.2 - - + +
118B VAL 3.7 6.8 + - - +
119B CYS* 3.5 18.4 - - - -
120B ARG* 3.2 25.6 + - - -
121B ILE* 2.9 32.5 + - + +
123B THR* 1.3 80.2 - - + +
125B LEU* 1.3 58.0 + - - +
128B PHE* 3.0 25.1 + - - +
13F C 3.5 29.0 + + - -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 4.6 12.3 - - + -
119B CYS* 4.0 10.7 - - + +
121B ILE 3.5 2.5 + - - +
122B PRO* 2.9 13.0 + - + +
124B HIS* 1.3 76.9 - - - +
126B PHE* 1.3 61.8 + - + +
128B PHE* 2.9 17.1 + - + +
129B ILE* 2.8 55.4 + - + +
152B VAL* 4.6 10.8 - - + -
155B TRP* 3.9 47.6 - - + +
156B TYR* 4.7 4.5 - - + +
179B HIS* 6.2 0.7 - - + -
182B LEU* 3.7 24.7 - - + -
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO* 2.8 37.6 + - + -
123B THR* 3.6 4.9 - - - +
125B LEU* 1.3 72.6 - - + +
127B THR* 1.3 59.2 + - - +
129B ILE* 3.9 4.3 - - - +
130B GLN* 3.0 30.5 + - - +
171B TYR 4.3 1.3 - - - -
173B GLN* 4.0 6.1 - - - -
174B ARG* 3.5 44.0 - - + +
175B ASN* 4.4 4.7 - - - +
177B TRP* 3.5 37.9 - - + -
178B SER* 3.8 15.7 - - - -
179B HIS* 3.5 29.6 - + - -
182B LEU* 3.4 31.0 - - + -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 4.2 19.2 + - + +
93B LEU* 3.7 21.5 - - + -
123B THR* 2.8 22.0 + - - +
126B PHE* 1.3 75.9 - - - +
128B PHE* 1.3 61.2 + - - +
130B GLN* 3.9 5.4 - - - +
131B PHE* 3.2 48.8 + - + -
175B ASN* 3.1 21.1 + - - -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.8 25.8 - - + -
96B LEU* 3.2 45.1 - - + -
97B ALA* 3.6 9.4 - - + -
100B SER* 4.0 9.9 - - - -
112B PHE* 4.5 4.9 - + - -
115B VAL* 4.0 17.7 - - + -
119B CYS* 4.3 9.2 - - - -
124B HIS 3.0 14.5 + - - +
125B LEU* 2.9 26.3 + - + +
127B THR* 1.3 75.2 - - - +
129B ILE* 1.3 70.5 + - + +
131B PHE* 3.1 15.3 + - - +
132B LYS* 3.1 39.2 + - + +
148B LEU* 4.6 10.8 - - + -
151B ALA* 6.0 0.7 - - + -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 2.8 46.7 + - + +
126B PHE* 3.9 2.7 - - - +
128B PHE* 1.3 78.1 - - + +
130B GLN* 1.3 63.5 + - - +
132B LYS* 3.3 9.9 + - + +
133B LYS* 3.2 18.5 + - - +
144B TRP* 3.8 15.9 - - + -
148B LEU* 4.5 13.0 - - + -
152B VAL* 3.8 17.7 - - + -
177B TRP* 3.4 46.4 - - + -
182B LEU* 3.7 22.4 - - + -
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Residues in contact with GLN 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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126B PHE 3.0 18.3 + - - +
127B THR* 3.9 6.7 - - - +
129B ILE* 1.3 75.0 - - - +
131B PHE* 1.3 64.4 + - + +
133B LYS* 3.2 24.7 + - - +
134B ASP* 3.0 50.5 + - - +
175B ASN* 5.1 13.3 + - + +
177B TRP* 3.4 26.2 + - + +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 3.4 37.5 - - + -
93B LEU 3.8 4.5 - - - -
94B PHE* 3.4 45.5 - + + -
97B ALA* 3.7 13.7 - - + -
127B THR* 3.2 36.0 + - + -
128B PHE 3.1 8.8 + - - +
130B GLN* 1.3 77.6 - - + +
132B LYS* 1.3 67.1 + - - +
134B ASP* 3.2 18.3 + - + +
135B LEU* 3.0 30.5 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 4.4 6.3 - - + -
100B SER* 2.5 34.4 + - - +
101B GLN* 2.9 43.9 + - - +
112B PHE* 4.3 6.9 - - + -
128B PHE* 3.1 42.7 + - + +
129B ILE* 3.5 10.3 - - + +
130B GLN 3.3 0.4 - - - -
131B PHE* 1.3 76.0 - - - +
133B LYS* 1.3 51.8 + - - +
135B LEU* 3.3 2.5 + - - -
136B LYS* 2.7 35.8 + - - +
148B LEU* 3.8 35.2 - - + -
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Residues in contact with LYS 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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129B ILE 3.2 10.2 + - - +
130B GLN* 3.3 29.6 + - - +
131B PHE 3.0 0.4 - - - -
132B LYS* 1.3 74.2 - - - +
134B ASP* 1.3 67.7 + - - +
135B LEU 3.0 1.6 - - - -
136B LYS* 2.9 29.9 + - + +
177B TRP* 3.9 21.1 - - + -
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Residues in contact with ASP 134 (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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94B PHE* 6.1 2.2 - - + -
130B GLN* 3.0 45.3 + - - +
131B PHE* 3.2 22.9 + - + +
133B LYS* 1.3 76.0 - - - +
135B LEU* 1.3 62.9 + - + +
136B LYS 4.8 1.6 - - - +
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Residues in contact with LEU 135 (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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94B PHE* 4.1 24.7 - - + -
97B ALA* 3.9 12.8 - - + -
98B VAL* 3.8 39.9 - - + +
101B GLN* 3.6 30.6 + - + +
131B PHE 3.0 18.9 + - - +
133B LYS 3.0 0.6 - - - -
134B ASP* 1.3 83.8 - - + +
136B LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 136 (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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101B GLN* 4.9 7.4 - - - +
132B LYS 2.7 17.8 + - - +
133B LYS* 2.9 21.2 + - + +
134B ASP 4.8 1.5 - - - +
135B LEU* 1.3 81.7 - - - +
144B TRP* 5.1 18.7 - - + +
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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