Contacts of the helix formed by residues 154 - 162 (chain A) in PDB entry 1YA8
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.5 30.3 - - - -
152A TYR 3.8 1.6 + - - -
153A ASP* 1.3 72.5 + - - +
155A LEU* 1.3 64.0 + - - +
156A ALA 3.2 3.4 + - - -
157A LEU* 3.3 4.5 + - - +
158A ALA* 3.0 26.2 + - - +
165A VAL* 4.2 16.8 - - - +
167A THR* 5.5 0.2 - - - +
476A PHE* 4.6 7.0 - - - -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A VAL* 3.7 35.9 - - + +
39A SER 4.7 0.9 - - - +
40A LEU* 4.2 29.6 - - + -
47A VAL* 3.6 32.3 - - + +
49A ILE* 4.5 9.0 - - + -
122A TYR* 3.6 7.1 - - - -
153A ASP* 3.0 22.6 + - - +
154A GLY* 1.3 76.2 - - - +
156A ALA* 1.3 61.4 + - - +
158A ALA* 3.8 3.1 + - - +
159A ALA* 3.2 23.7 + - - +
481A LEU* 4.4 12.6 - - + -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.7 18.8 - - + -
153A ASP 4.8 1.4 + - - -
154A GLY 3.3 0.8 - - - -
155A LEU* 1.3 76.3 - - - +
157A LEU* 1.3 59.6 + - - +
159A ALA 3.1 1.6 + - - -
160A HIS* 2.8 46.3 + - + -
476A PHE 4.1 8.1 - - - +
477A GLY* 3.8 26.5 - - - +
480A PHE* 4.3 8.1 - - + -
481A LEU* 4.5 10.6 - - + +
497A MET* 4.9 0.9 - - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A MET* 4.5 13.9 - - + -
153A ASP 5.5 0.2 + - - -
154A GLY* 3.3 9.8 + - - +
156A ALA* 1.3 77.5 - - - +
158A ALA* 1.3 62.6 + - - +
161A GLU* 3.0 44.3 + - + +
163A VAL* 4.1 7.3 - - + +
165A VAL* 4.0 19.5 - - + -
218A PHE* 4.4 24.9 - - + -
475A VAL* 4.0 19.7 - - + +
476A PHE* 4.8 16.4 + - + -
497A MET* 4.2 27.9 - - + +
500A TRP* 5.8 2.5 - - + -
501A ALA* 5.2 1.1 - - + +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.6 4.7 - - + -
122A TYR* 3.6 22.4 - - + +
124A PRO* 3.3 22.2 - - + +
154A GLY 3.0 17.1 + - - +
155A LEU 4.0 3.8 - - - +
157A LEU* 1.3 78.6 - - - +
159A ALA* 1.3 57.3 + - - +
162A ASN* 3.0 24.4 + - - -
163A VAL* 3.4 23.1 - - - +
165A VAL* 4.0 4.6 - - + +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.0 12.3 - - + -
43A PHE* 3.3 42.7 - - + -
47A VAL* 4.3 13.0 - - + +
124A PRO* 4.2 9.1 - - - +
155A LEU 3.2 16.7 + - - +
156A ALA 3.1 2.8 + - - +
158A ALA* 1.3 82.5 - - - +
160A HIS* 1.3 63.9 + - - +
162A ASN* 3.8 8.8 + - - +
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Residues in contact with HIS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.2 11.7 - - + +
41A GLU 5.1 1.6 + - - -
43A PHE* 3.6 32.6 - + - -
156A ALA* 2.8 38.0 + - + +
157A LEU 4.4 1.1 - - - +
159A ALA* 1.3 75.1 - - - +
161A GLU* 1.3 70.4 + - + +
480A PHE* 3.4 45.0 - + - -
494A LYS* 4.5 12.6 - - - +
497A MET* 4.1 23.4 - - + +
498A LYS* 5.4 1.4 + - - -
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.0 21.4 + - + +
160A HIS* 1.3 85.1 - - + +
162A ASN* 1.3 71.9 + - - +
163A VAL* 3.3 5.0 - - + +
494A LYS 4.5 1.7 - - - +
497A MET* 3.7 23.1 - - + +
498A LYS* 3.0 46.1 + - - +
501A ALA* 3.4 20.9 - - + -
505A ARG* 2.9 48.7 + - - -
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Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 3.9 20.9 + - - +
125A ALA* 5.7 0.4 - - - +
133A LEU* 3.3 45.0 - - - +
134A PRO* 3.9 3.6 - - - +
158A ALA 3.0 10.9 + - - -
159A ALA 3.8 6.0 + - - +
160A HIS 3.6 1.8 - - - -
161A GLU* 1.3 82.3 - - - +
163A VAL* 1.3 61.5 + - - +
505A ARG* 4.7 1.9 + - - +
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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