Contacts of the helix formed by residues 124 - 138 (chain B) in PDB entry 2Y96
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 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B HIS* 6.3 0.7 - - - -
111B VAL* 3.5 46.4 - - + -
112B GLU 5.1 5.2 - - - -
119B PHE* 4.0 23.6 - + - -
120B ASP 4.9 0.2 - - - -
121B LEU* 2.9 21.2 + - + +
123B VAL* 1.3 99.4 - - + +
125B PHE* 1.3 64.5 + - - +
126B TYR 3.3 2.5 - - - -
127B PRO* 3.7 13.0 - - + -
128B ALA* 2.9 27.9 + - + +
157B LEU* 4.4 8.7 - - + -
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.4 23.3 - - + -
122B SER* 3.3 34.9 + - - +
124B PHE* 1.3 75.6 - - - +
126B TYR* 1.3 64.6 + + + +
128B ALA* 4.1 0.3 - - - +
129B ALA* 2.9 32.1 + - - +
156B THR* 3.7 32.1 - - + -
157B LEU* 4.0 10.9 - - + +
160B ALA* 3.7 21.9 - - + +
164B ILE* 4.0 10.2 - - + +
192B GLN* 3.9 29.6 - - + -
193B LEU* 4.1 6.5 - - + -
196B LEU* 3.9 29.4 - - + -
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Residues in contact with TYR 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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122B SER 4.9 3.5 + - - -
125B PHE* 1.3 80.8 - - + +
127B PRO* 1.3 68.2 - - + +
129B ALA* 3.7 1.2 - - - +
130B ALA* 2.9 29.7 + - - +
164B ILE* 3.7 39.7 - - + -
165B HIS* 5.2 1.8 + - - -
196B LEU* 3.8 18.2 - - + +
199B GLN* 5.3 4.0 + - - +
200B LEU* 3.8 23.9 - - - +
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Residues in contact with PRO 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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123B VAL 4.0 15.5 - - - +
124B PHE* 3.5 20.0 - - + +
126B TYR* 1.3 93.6 - - + +
128B ALA* 1.3 64.8 + - - +
130B ALA* 3.4 8.0 + - + +
131B PHE* 3.1 22.0 + - - +
134B ARG* 5.0 1.4 + - - -
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Residues in contact with ALA 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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85B LEU* 4.2 12.5 - - + +
111B VAL* 5.1 6.5 - - + -
124B PHE* 2.9 22.8 + - + +
125B PHE 4.1 0.7 - - - +
127B PRO* 1.3 75.4 - - - +
129B ALA* 1.3 63.7 + - - +
131B PHE* 3.1 10.4 + - - +
132B ILE* 3.0 26.5 + - + +
157B LEU* 3.9 35.9 - - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE 2.9 20.7 + - - +
126B TYR 3.8 2.7 - - - +
128B ALA* 1.3 75.8 - - - +
130B ALA* 1.3 52.5 + - - +
132B ILE* 3.2 2.7 + - - -
133B ASP* 2.8 35.9 + - - +
157B LEU 5.4 1.0 + - - +
161B TYR* 3.5 33.1 - - - +
164B ILE* 4.1 11.2 - - + -
165B HIS* 3.6 22.9 - - + +
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Residues in contact with ALA 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 TYR 2.9 18.0 + - - +
127B PRO* 3.7 8.5 - - + +
128B ALA 3.2 0.2 - - - -
129B ALA* 1.3 75.4 - - - +
131B PHE* 1.3 57.4 + - - +
133B ASP* 3.8 3.1 - - - +
134B ARG* 3.0 49.6 + - - +
165B HIS* 4.1 11.1 + - + +
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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
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83B HIS* 4.1 26.9 - + + -
84B VAL 4.2 7.2 - - - -
85B LEU* 4.1 26.2 - - + -
107B GLN* 4.1 24.5 - - + -
108B TYR 4.5 3.1 - - - -
109B HIS* 3.9 26.0 - + + -
127B PRO 3.1 12.2 + - - +
128B ALA* 3.1 12.7 + - - +
130B ALA* 1.3 78.6 - - - +
132B ILE* 1.3 62.7 + - - +
134B ARG* 3.3 25.1 + - - +
135B ALA* 3.0 23.4 + - - +
143B ILE* 3.9 24.5 - - + -
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Residues in contact with ILE 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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62B LEU* 3.9 11.0 - - + -
85B LEU* 4.0 18.6 - - + -
128B ALA 3.0 20.0 + - - +
129B ALA 3.6 5.6 - - - +
131B PHE* 1.3 74.7 - - - +
133B ASP* 1.3 64.3 + - - +
135B ALA* 3.2 2.4 + - - +
136B LEU* 3.0 36.8 + - + +
143B ILE* 4.0 24.5 - - + -
145B VAL* 4.2 12.6 - - + -
157B LEU* 4.2 12.6 - - + +
158B VAL* 4.5 7.4 - - + -
161B TYR* 3.7 45.3 - - + -
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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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129B ALA 2.8 20.6 + - - +
130B ALA* 3.8 4.7 - - - +
132B ILE* 1.3 72.0 - - - +
134B ARG* 1.3 59.2 + - - +
136B LEU* 3.4 2.6 + - - +
137B SER* 3.0 36.3 + - - -
161B TYR* 3.6 26.0 + - + -
165B HIS* 3.9 31.6 + - + +
166B LYS* 4.8 6.8 + - - -
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Residues in contact with ARG 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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107B GLN* 6.1 1.2 - - - +
127B PRO 5.0 1.4 + - - -
130B ALA* 3.0 37.1 + - - +
131B PHE* 3.5 36.4 - - - +
132B ILE 3.2 0.2 - - - -
133B ASP* 1.3 77.5 - - - +
135B ALA* 1.3 62.0 + - - +
137B SER* 3.3 21.4 - - - -
138B ASP* 4.0 3.3 + - - +
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Residues in contact with ALA 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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83B HIS* 3.6 44.2 - - + +
131B PHE 3.0 17.0 + - - +
132B ILE 3.6 4.0 - - - +
134B ARG* 1.3 80.2 - - - +
136B LEU* 1.3 60.6 + - - +
137B SER 3.4 0.3 + - - -
138B ASP* 3.4 5.4 + - - +
141B SER* 2.9 28.0 + - - -
143B ILE* 4.3 18.2 - - + -
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Residues in contact with LEU 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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59B TRP* 4.2 13.9 - - + +
60B PRO 3.8 4.3 - - - +
61B LYS* 3.8 38.1 - - + +
62B LEU* 4.1 15.0 - - + -
132B ILE* 3.0 30.1 + - + +
133B ASP* 3.7 3.6 - - - +
135B ALA* 1.3 74.3 - - - +
137B SER* 1.3 63.9 + - - +
138B ASP 3.2 9.9 + - - +
139B ASP* 5.3 0.5 - - - -
141B SER 4.7 5.2 - - - +
143B ILE* 4.0 12.3 - - + +
161B TYR* 3.5 26.5 - - + +
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Residues in contact with SER 137 (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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133B ASP* 3.0 20.6 + - - -
134B ARG* 3.3 17.0 - - - -
135B ALA 3.2 0.4 - - - -
136B LEU* 1.3 78.8 - - - +
138B ASP* 1.3 58.3 + - - +
139B ASP* 3.9 1.2 + - - -
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Residues in contact with ASP 138 (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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61B LYS* 6.1 0.3 - - - +
134B ARG 4.0 2.4 + - - +
135B ALA 3.4 13.0 + - - +
136B LEU* 3.2 8.9 - - - +
137B SER* 1.3 79.3 - - - +
139B ASP* 1.3 80.4 + - - +
140B HIS* 2.9 25.9 + - - +
141B SER* 3.5 25.3 + - - +
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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