Contacts of the helix formed by residues 128 - 139 (chain B) in PDB entry 1YH3
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 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B TRP* 3.8 4.4 - - + -
126B SER 3.6 7.9 - - - +
127B ARG* 1.3 78.3 - - - +
129B LYS* 1.3 65.7 + - - +
130B ASP 3.4 2.4 + - - -
131B LEU* 3.9 22.9 - - + +
132B ALA* 3.2 17.2 + - - +
207B MET* 3.5 44.2 - - + +
208B LEU 4.1 2.7 - - - +
209B ASP* 3.5 30.1 - - + +
243B ILE* 3.8 24.9 - - + -
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Residues in contact with LYS 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 TRP* 3.4 42.3 - - + -
127B ARG 3.7 1.6 - - - -
128B ILE* 1.3 74.7 - - - +
130B ASP* 1.3 73.5 + - - +
132B ALA* 3.2 3.6 + - - +
133B HIS* 2.8 47.1 + - + -
155B ASP* 2.6 35.6 + - - -
156B ASP* 2.9 28.1 + - - +
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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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128B ILE 3.4 0.8 - - - -
129B LYS* 1.3 89.6 - - - +
131B LEU* 1.3 57.6 + - - +
133B HIS* 3.3 4.3 + - - +
134B GLN* 2.9 48.8 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 3.6 16.3 + - + +
129B LYS 3.6 0.4 - - - -
130B ASP* 1.3 72.4 - - - +
132B ALA* 1.3 64.8 + - - +
134B GLN* 4.0 9.3 + - - +
135B PHE* 3.1 20.3 + - - +
207B MET* 3.7 22.8 - - + +
243B ILE* 3.6 46.4 - - + -
281B PRO* 4.4 16.4 - - + +
284B PHE* 4.0 14.4 - - + -
285B LEU* 4.0 26.5 - - + -
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Residues in contact with ALA 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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123B LEU* 4.0 10.7 - - + +
125B TRP* 3.7 35.7 - - + -
128B ILE 3.2 13.1 + - - +
129B LYS 3.2 10.3 + - - +
131B LEU* 1.3 76.4 - - - +
133B HIS* 1.3 64.7 + - + +
135B PHE* 3.2 17.2 + - - +
136B THR* 3.3 14.0 + - - +
144B THR* 4.4 3.1 - - + -
207B MET* 3.8 14.7 - - - -
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TRP* 3.7 12.9 - + - -
129B LYS* 2.8 56.5 + - + +
130B ASP* 4.2 2.7 - - - +
132B ALA* 1.3 72.1 - - - +
134B GLN* 1.3 66.9 + - - +
135B PHE 3.1 1.3 - - - -
136B THR* 3.3 5.8 + - - +
137B GLN* 2.9 34.4 + - + +
144B THR* 3.2 21.2 + - + +
146B GLU* 2.8 43.3 + - + +
147B ASP* 4.4 7.1 + - - +
155B ASP* 5.7 1.1 - - - -
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Residues in contact with GLN 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* 2.9 33.4 + - - +
131B LEU* 4.0 14.1 + - - +
133B HIS* 1.3 76.0 - - - +
135B PHE* 1.3 61.7 + - - +
137B GLN* 3.3 9.8 + - - +
138B VAL* 3.2 26.5 + - - +
285B LEU* 4.1 28.4 - - + +
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Residues in contact with PHE 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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123B LEU* 3.9 17.3 - - + -
131B LEU 3.1 15.1 + - - +
132B ALA* 3.3 10.3 - - - +
133B HIS 3.1 1.0 - - - -
134B GLN* 1.3 77.4 - - - +
136B THR* 1.3 62.9 + - + +
137B GLN 3.1 0.2 - - - -
138B VAL* 3.1 4.8 + - - +
139B GLN* 2.8 30.3 + - - -
142B MET* 4.3 31.4 - - + -
207B MET* 4.3 9.0 - - + -
241B TRP* 3.8 24.0 - + - -
284B PHE* 3.9 21.5 - + - -
285B LEU* 4.1 8.3 - - + +
288B VAL* 3.6 39.5 - - + -
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Residues in contact with THR 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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123B LEU* 4.2 4.3 - - + -
132B ALA 3.3 13.0 + - - +
133B HIS* 3.3 12.6 + - - -
135B PHE* 1.3 84.0 - - + +
137B GLN* 1.3 64.3 + - - +
139B GLN 4.1 9.2 - - - -
140B ARG* 3.6 18.0 - - - +
142B MET* 3.5 27.4 - - + +
143B PHE 4.3 0.9 - - - +
144B THR* 3.7 14.1 - - + +
147B ASP* 2.9 34.8 + - - +
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Residues in contact with GLN 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 HIS* 2.9 30.2 + - + +
134B GLN* 3.5 9.9 - - - +
135B PHE 3.1 0.2 - - - -
136B THR* 1.3 82.7 - - - +
138B VAL* 1.3 64.3 + - + +
140B ARG* 4.4 3.1 + - - -
147B ASP* 5.7 3.6 - - - +
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Residues in contact with VAL 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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134B GLN 3.2 13.4 + - - +
135B PHE 3.1 5.6 + - - +
137B GLN* 1.3 79.1 - - + +
139B GLN* 1.3 54.3 + - - +
140B ARG* 2.7 17.4 + - - -
285B LEU* 4.6 4.9 - - + -
288B VAL* 3.7 19.5 - - + +
289B LYS* 3.4 63.5 - - + +
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Residues in contact with GLN 139 (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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135B PHE* 2.8 22.3 + - - -
136B THR* 4.1 5.1 - - - -
138B VAL* 1.3 70.6 - - - +
140B ARG* 1.3 56.2 + - - +
141B ASP 2.9 11.3 + - - -
142B MET* 2.9 26.8 + - - +
288B VAL* 4.4 7.7 - - - +
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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