Contacts of the helix formed by residues 123 - 135 (chain B) in PDB entry 2Y05
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 GLY 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B LEU* 5.9 1.6 - - - -
118B ALA 3.5 16.6 - - - -
120B GLY 3.0 8.7 + - - -
121B THR 3.4 0.4 - - - -
122B VAL* 1.3 78.2 - - - +
124B MET* 1.3 66.2 + - - -
126B GLY 3.1 2.3 + - - -
127B LEU* 2.9 30.4 + - - +
280B ARG* 6.3 0.7 - - - -
284B LEU* 3.9 10.3 - - - +
287B LEU* 5.1 0.2 - - - +
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Residues in contact with MET 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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47B ASP* 4.2 20.0 - - + +
49B TYR* 4.3 20.2 - - + -
66B GLN* 4.5 15.6 + - - +
118B ALA 4.5 3.2 + - - -
119B LEU 4.7 0.6 - - - -
123B GLY* 1.3 72.2 - - - +
125B PRO* 1.4 71.9 - - + +
127B LEU* 3.2 11.6 + - - +
128B THR* 2.9 32.1 + - - -
272B VAL* 3.7 20.5 - - + +
273B TYR* 3.9 27.8 - - + +
701B NAP 3.7 33.7 - - + -
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 4.4 6.5 - - - +
119B LEU 3.3 24.2 - - - +
120B GLY* 3.6 9.4 - - - +
124B MET* 1.4 102.3 - - + +
126B GLY* 1.3 57.1 + - - +
128B THR* 3.3 9.9 + - - +
129B ALA* 3.0 27.0 + - - +
153B ALA* 3.8 24.7 - - + -
154B VAL* 3.8 18.2 - - + +
324B LYS* 4.0 17.7 - - + -
701B NAP 4.8 3.8 - - + +
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Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLY 3.1 12.3 + - - -
121B THR* 3.4 25.1 - - - +
123B GLY 3.6 0.2 - - - -
125B PRO* 1.3 72.6 - - - +
127B LEU* 1.3 60.2 + - - +
129B ALA* 3.4 7.0 + - - +
130B TYR* 2.9 28.1 + - - +
157B VAL* 4.4 10.1 - - - +
287B LEU* 3.6 12.3 - - - +
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Residues in contact with LEU 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 GLY* 2.9 20.7 + - - +
124B MET* 3.6 10.1 - - + +
126B GLY* 1.3 72.6 - - - +
128B THR* 1.3 60.4 + - - +
130B TYR* 4.1 2.7 - - - -
131B PHE* 2.9 47.0 + - + +
272B VAL* 3.7 15.3 - - + -
275B TRP 5.9 0.2 - - - +
280B ARG* 3.9 36.8 - - + +
283B ALA* 3.4 33.2 - - + -
284B LEU* 3.8 32.1 - - + +
287B LEU* 3.8 3.1 - - + +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B MET* 2.9 15.7 + - - -
125B PRO* 3.3 11.2 - - - -
126B GLY 3.3 0.2 - - - -
127B LEU* 1.3 74.3 - - - +
129B ALA* 1.3 58.5 + - - +
131B PHE* 5.4 0.4 - - - -
132B GLY* 3.0 27.8 + - - +
154B VAL* 3.9 7.6 - - + -
215B PHE* 3.9 1.6 - - - -
239B CYS* 3.3 34.1 - - - -
270B PHE* 3.7 11.4 - - + -
272B VAL* 3.4 16.1 - - - +
701B NAP 3.3 32.2 - - + -
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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
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125B PRO 3.0 11.6 + - - +
126B GLY 3.6 7.6 - - - +
128B THR* 1.3 73.9 - - - +
130B TYR* 1.3 67.5 + - - +
133B LEU* 3.0 28.8 + - - +
154B VAL* 3.6 13.7 - - - +
157B VAL* 3.6 13.2 - - + -
158B VAL* 3.5 38.3 - - + +
161B ILE* 4.5 2.5 - - - +
215B PHE* 4.1 2.1 - - - -
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Residues in contact with TYR 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 GLY 2.9 19.0 + - - +
127B LEU* 3.2 8.7 + - - +
129B ALA* 1.3 75.8 - - - +
131B PHE* 1.3 77.7 + + - +
134B LEU* 2.9 53.4 + - + +
135B GLU* 6.2 0.7 - - + -
161B ILE* 3.9 10.9 - - + +
279B ALA 5.4 0.2 - - - -
282B LYS* 4.9 4.3 - - - +
283B ALA* 3.7 29.6 + - + -
286B ASP* 2.6 41.9 + - + -
287B LEU* 4.2 13.5 - - + -
290B TRP* 3.7 26.6 - + - -
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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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127B LEU* 2.9 42.5 + - + +
128B THR* 4.8 1.1 - - - +
130B TYR* 1.3 86.7 - + - +
132B GLY* 1.3 60.6 + - - +
135B GLU* 2.9 44.4 + - + +
136B ILE* 3.1 9.3 + - - +
270B PHE* 5.5 0.2 - - + -
272B VAL 5.0 2.5 - - - -
275B TRP* 3.4 79.2 - + + -
279B ALA* 3.7 18.6 - - + -
280B ARG* 4.5 3.1 - - + -
283B ALA* 3.6 29.8 - - + -
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Residues in contact with GLY 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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128B THR 3.0 18.5 + - - -
131B PHE* 1.3 76.7 - - - +
133B LEU* 1.3 56.3 + - - +
136B ILE* 3.3 9.0 - - - +
137B CYS* 2.9 25.6 + - - -
215B PHE* 3.7 9.4 - - - -
237B ALA* 3.8 5.4 - - - +
270B PHE* 3.6 27.6 - - - -
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Residues in contact with LEU 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 3.0 18.7 + - - +
130B TYR 4.3 0.4 - - - +
132B GLY* 1.3 76.3 - - - +
134B LEU* 1.3 59.6 + - + +
137B CYS* 3.3 15.4 - - + +
138B GLY 3.1 21.5 + - - -
139B VAL* 3.4 39.1 + - + -
145B VAL* 4.1 23.8 - - + -
158B VAL* 3.5 33.0 - - + +
161B ILE* 3.7 17.3 - - + -
162B ALA* 3.6 22.4 - - + +
215B PHE* 3.7 8.8 - - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 2.9 57.9 + - + +
133B LEU* 1.3 78.8 - - + +
135B GLU* 1.3 62.3 + - + +
138B GLY* 3.3 17.0 - - - -
139B VAL* 3.8 29.3 - - + +
140B LYS* 6.0 0.3 + - - -
161B ILE* 3.9 28.7 - - + -
165B LYS* 4.1 20.6 - - + +
290B TRP* 4.6 5.8 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 6.2 0.7 - - + -
131B PHE* 2.9 38.7 + - + +
134B LEU* 1.3 79.5 - - + +
136B ILE* 1.3 67.5 + - + +
138B GLY* 3.6 7.2 + - - -
266B ARG* 6.0 0.2 + - - -
275B TRP* 2.9 37.9 + - + -
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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