Contacts of the helix formed by residues 120 - 135 (chain B) in PDB entry 1YHQ
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 ASP 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28210 C 4.6 1.2 + - - -
119B HIS* 1.3 83.4 + - - +
121B PRO* 1.3 62.6 - - - +
122B ASP* 3.3 10.9 + - - +
123B ALA* 2.7 43.1 + - + +
124B ALA* 3.2 19.2 + - - +
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Residues in contact with PRO 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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100B VAL* 3.8 19.8 - - + +
101B TRP 4.0 10.5 - - - +
102B THR* 5.8 1.1 - - - -
103B ASP* 5.6 5.6 - - - +
119B HIS* 3.3 34.3 - - + +
120B ASP* 1.3 86.2 - - - +
122B ASP* 1.3 66.0 + - - +
124B ALA* 3.5 2.9 + - - +
125B GLU* 2.8 31.2 + - - +
183B GLU* 5.0 9.9 - - - +
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Residues in contact with ASP 122 (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 ASP* 3.3 7.3 + - - +
121B PRO* 1.3 83.5 - - - +
123B ALA* 1.3 59.0 + - - +
125B GLU* 3.5 16.6 - - - +
126B GLU* 2.6 38.5 + - - +
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Residues in contact with ALA 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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120B ASP* 2.7 41.2 + - + +
122B ASP* 1.3 72.7 - - - +
124B ALA* 1.3 63.1 + - - +
126B GLU* 3.4 9.7 + - - +
127B GLN* 3.0 22.2 + - - +
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Residues in contact with ALA 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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28200 A 6.3 0.2 - - - -
98B THR* 4.0 15.3 + - + -
99B GLU 3.2 27.4 - - - +
100B VAL* 3.9 6.7 - - + -
119B HIS* 4.5 4.9 - - + -
120B ASP 3.2 10.0 + - - +
121B PRO 3.6 7.9 - - - +
122B ASP 3.2 0.2 - - - -
123B ALA* 1.3 76.6 - - - +
125B GLU* 1.3 66.5 + - - +
127B GLN* 3.1 9.5 + - - +
128B ILE* 3.0 27.5 + - + +
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Residues in contact with GLU 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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100B VAL* 3.9 11.1 - - + +
121B PRO 2.8 20.8 + - - +
122B ASP* 3.5 18.1 - - - +
124B ALA* 1.3 77.1 - - - +
126B GLU* 1.3 62.1 + - - +
128B ILE* 3.1 8.6 + - + +
129B ARG* 2.7 59.4 + - + +
175B LEU* 5.5 1.1 - - + -
179B LEU* 3.5 35.9 - - + +
183B GLU* 4.5 10.2 - - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP 2.6 22.5 + - - +
123B ALA* 3.5 9.8 - - - +
125B GLU* 1.3 73.4 - - - +
127B GLN* 1.3 63.0 + - - +
129B ARG* 3.1 9.3 + - + +
130B ASP* 2.9 43.4 + - - +
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Residues in contact with GLN 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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97B LEU* 3.3 27.8 - - + +
98B THR* 2.8 33.6 - - - +
123B ALA 3.0 13.9 + - - +
124B ALA* 3.1 9.5 + - - +
126B GLU* 1.3 75.4 - - - +
128B ILE* 1.3 57.9 + - - +
130B ASP* 3.5 9.3 + - - +
131B ALA* 3.1 26.2 + - - +
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Residues in contact with ILE 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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84B LEU* 3.7 25.6 - - + +
86B ALA* 3.6 33.7 - - + -
97B LEU* 4.9 3.6 - - + -
98B THR* 3.9 14.1 - - - +
100B VAL* 3.9 18.8 - - + -
124B ALA 3.0 11.3 + - - +
125B GLU* 3.3 9.9 - - + +
127B GLN* 1.3 74.7 - - - +
129B ARG* 1.3 61.5 + - + +
131B ALA* 3.1 9.5 + - - +
132B HIS* 2.9 25.3 + - - +
137B LEU* 4.3 12.0 - - + +
140B LEU* 4.9 1.6 - - + -
175B LEU* 4.2 26.9 - - + -
179B LEU* 6.0 0.4 - - + -
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Residues in contact with ARG 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 GLU* 2.7 57.9 + - + +
126B GLU* 3.8 7.9 - - + +
128B ILE* 1.3 73.8 - - + +
130B ASP* 1.3 66.6 + - - +
132B HIS* 3.2 9.7 + - - +
133B GLU* 3.0 30.9 + - + +
172B SER* 4.9 2.8 + - - +
175B LEU* 4.3 23.5 - - + +
176B ASP* 2.9 30.3 + - - -
179B LEU* 3.8 10.1 - - - +
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Residues in contact with ASP 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 GLU* 2.9 41.6 + - - +
127B GLN* 3.8 8.1 - - - +
129B ARG* 1.3 74.8 - - - +
131B ALA* 1.3 63.4 + - - +
133B GLU* 3.2 22.9 + - - +
134B ALA* 3.1 22.4 + - - +
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Residues in contact with ALA 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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97B LEU* 3.6 26.2 - - + -
127B GLN 3.1 14.4 + - - +
128B ILE 3.1 9.8 + - - +
130B ASP* 1.3 77.8 - - - +
132B HIS* 1.3 60.4 + - - +
134B ALA* 3.2 8.0 + - - +
135B GLY 3.0 16.6 + - - -
136B ASP* 3.2 17.1 + - + -
137B LEU* 4.5 13.5 - - + +
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Residues in contact with HIS 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 ILE 2.9 12.3 + - - +
129B ARG* 3.2 12.5 + - + +
131B ALA* 1.3 76.0 - - - +
133B GLU* 1.3 66.1 + - + +
135B GLY* 3.1 13.6 + - - +
137B LEU* 3.9 27.9 - - + +
171B VAL* 3.1 30.2 - - + +
172B SER* 3.0 31.3 + - - -
175B LEU* 5.0 9.6 - - + -
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Residues in contact with GLU 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 ARG* 3.0 20.4 + - + +
130B ASP* 3.4 26.2 - - - +
131B ALA 3.2 0.2 - - - -
132B HIS* 1.3 79.6 - - + +
134B ALA* 1.3 63.1 + - - +
135B GLY* 3.0 1.4 + - - -
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Residues in contact with ALA 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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130B ASP 3.1 9.4 + - - +
131B ALA* 3.2 10.7 + - - +
133B GLU* 1.3 79.5 - - - +
135B GLY* 1.3 61.5 + - - +
136B ASP* 3.4 24.0 - - - +
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Residues in contact with GLY 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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89B ASP* 5.4 1.9 - - - +
131B ALA 3.0 3.8 + - - -
132B HIS* 3.1 11.6 + - - -
133B GLU 3.0 5.5 - - - -
134B ALA* 1.3 80.2 - - - +
136B ASP* 1.3 65.2 + - - +
137B LEU 3.6 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