Contacts of the helix formed by residues 143 - 154 (chain B) in PDB entry 1Y7M
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 HIS 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PRO* 4.0 15.3 + - + +
125B THR* 4.8 2.9 - - - -
128B PRO* 4.1 21.6 + - + +
131B ILE* 3.6 39.2 - - + +
142B MSE 1.3 75.7 - - - +
144B ASN* 1.3 66.4 + - - +
145B LYS* 4.3 5.8 - - + -
146B ASP* 3.1 28.2 + - - +
147B VAL* 3.1 18.4 + - - +
206B SO4 3.9 25.8 - - - +
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Residues in contact with ASN 144 (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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109B GLY* 4.3 3.4 - - - -
110B ALA* 2.9 37.0 + - + +
124B GLY* 3.5 1.2 - - - -
125B THR* 3.1 37.6 + - - +
126B ASN* 5.3 0.6 - - - +
142B MSE 3.6 0.8 + - - -
143B HIS* 1.3 71.1 - - - +
145B LYS* 1.3 64.2 + - - +
147B VAL* 3.3 6.4 - - - +
148B ILE* 3.0 32.3 + - + +
206B SO4 5.3 0.6 + - - -
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Residues in contact with LYS 145 (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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143B HIS* 4.3 6.1 - - + -
144B ASN* 1.3 78.6 - - - +
146B ASP* 1.3 80.3 + - - +
148B ILE* 3.7 10.9 + - - +
149B GLU* 3.2 26.0 + - - +
206B SO4 3.3 48.1 + - - +
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 3.3 39.5 - - + +
80B PRO* 4.0 13.2 - - - +
142B MSE 3.8 13.2 - - + +
143B HIS* 3.1 33.6 + - + +
145B LYS* 1.3 97.6 + - - +
147B VAL* 1.3 61.2 + - - +
149B GLU* 3.2 5.6 + - - +
150B LEU* 2.8 29.5 + - - +
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Residues in contact with VAL 147 (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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110B ALA* 4.2 2.0 - - + -
111B TYR* 3.7 22.4 - - + +
113B LEU* 3.4 31.2 - - + -
122B ILE* 4.6 0.7 - - + -
123B HIS* 4.2 4.5 - - - -
124B GLY* 3.8 31.6 - - - +
142B MSE 4.0 23.7 - - + +
143B HIS 3.1 10.6 + - - +
144B ASN* 3.3 13.7 - - - +
146B ASP* 1.3 74.9 - - - +
148B ILE* 1.3 68.5 + - - +
150B LEU* 4.2 1.8 - - + -
151B ALA* 2.9 23.9 + - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 3.7 24.7 - - + +
111B TYR* 4.3 19.2 - - + -
144B ASN* 3.0 26.6 + - + +
145B LYS* 3.7 9.0 - - - +
147B VAL* 1.3 76.6 - - - +
149B GLU* 1.3 58.9 + - - +
151B ALA* 3.8 1.9 - - - +
152B SER* 3.0 30.3 + - - -
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Residues in contact with GLU 149 (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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77B LYS* 3.1 30.8 + - - +
79B TYR* 2.6 33.8 + - - +
145B LYS 3.2 16.4 + - - +
146B ASP* 3.6 5.8 - - - +
147B VAL 3.2 0.2 - - - -
148B ILE* 1.3 77.6 - - - +
150B LEU* 1.3 66.5 + - - +
152B SER* 2.6 26.4 + - - +
153B ILE* 3.3 18.6 + - + +
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Residues in contact with LEU 150 (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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58B ILE* 4.0 24.7 - - + -
67B LEU* 4.3 23.6 - - + -
69B LEU* 4.4 11.4 - - + -
79B TYR* 4.2 15.8 + - + -
113B LEU* 4.2 19.7 - - + -
122B ILE* 4.3 9.0 - - + -
142B MSE 3.7 25.8 - - - -
146B ASP 2.8 19.9 + - - +
147B VAL* 3.7 4.9 - - - +
149B GLU* 1.3 73.3 - - - +
151B ALA* 1.3 61.4 + - - +
153B ILE* 3.2 7.1 + - - +
154B VAL* 3.1 41.5 + - + +
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Residues in contact with ALA 151 (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 ARG* 3.3 30.9 + - - +
111B TYR* 3.9 34.5 - - + -
113B LEU* 4.6 14.1 - - + +
147B VAL 2.9 17.5 + - - +
148B ILE 3.8 3.6 - - - +
150B LEU* 1.3 76.8 - - - +
152B SER* 1.3 64.9 + - - +
153B ILE 3.1 1.2 + - - -
154B VAL* 3.5 7.9 - - - +
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Residues in contact with SER 152 (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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111B TYR* 5.9 0.2 - - - -
148B ILE* 3.0 18.6 + - - -
149B GLU* 2.6 22.9 + - - +
151B ALA* 1.3 75.6 - - - +
153B ILE* 1.3 66.0 + - - +
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Residues in contact with ILE 153 (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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56B TYR* 3.5 46.0 + - + +
69B LEU* 4.1 18.4 - - + -
76B MSE 3.4 27.8 - - + -
77B LYS* 5.0 2.0 - - - -
79B TYR* 5.1 0.9 - - - +
149B GLU* 3.5 32.1 - - + +
150B LEU* 3.2 5.7 + - - +
151B ALA 3.1 0.6 - - - -
152B SER* 1.3 87.3 - - - +
154B VAL* 1.3 66.1 + - + +
155B PRO* 3.8 1.9 - - - +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 4.1 12.8 - - + -
58B ILE* 4.2 21.1 - - + -
69B LEU* 3.4 38.1 - - + -
97B ILE* 4.9 3.4 - - + -
100B ARG* 3.0 26.6 + - - +
113B LEU* 4.7 12.8 - - + -
150B LEU* 3.1 24.5 + - + +
151B ALA* 3.5 3.0 - - - +
153B ILE* 1.3 77.3 - - - +
155B PRO* 1.3 64.7 - - + +
158B THR* 3.6 15.0 - - + +
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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