Contacts of the helix formed by residues 146 - 153 (chain A) in PDB entry 4Y1W
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 LEU 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.8 17.9 - - - +
34A VAL* 3.9 35.0 - - + +
37A LEU* 4.0 21.8 - - + -
38A ALA 4.3 6.7 - - - +
116A TYR* 4.2 2.0 - - - -
144A SER* 3.0 12.2 + - - +
145A THR* 1.3 94.0 - - - +
147A PRO* 1.3 72.4 - - - +
148A GLU* 3.9 8.5 - - + +
149A VAL* 3.1 18.8 + - + +
150A ALA* 3.4 8.7 + - - +
189A GLU* 4.0 20.4 - - + -
190A ALA* 4.1 8.3 - - + -
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Residues in contact with PRO 147 (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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23A ALA* 3.6 33.2 - - + +
24A ILE* 4.6 6.7 - - + -
29A ARG* 3.7 11.7 - - - +
116A TYR* 3.8 35.9 - - + -
145A THR 3.6 8.7 - - - +
146A LEU* 1.3 84.6 - - - +
148A GLU* 1.3 73.2 + - - +
150A ALA* 3.2 2.6 + - - +
151A LYS* 3.0 35.2 + - + +
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Residues in contact with GLU 148 (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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27A PRO 4.6 1.0 - - - +
28A ASN* 3.5 45.7 + - + +
29A ARG* 2.8 63.6 + - - +
34A VAL* 3.9 22.0 - - + +
146A LEU* 3.9 5.4 - - - +
147A PRO* 1.3 80.7 - - - +
149A VAL* 1.3 66.2 - - + +
151A LYS* 3.4 5.6 + - - +
152A ARG* 3.3 30.4 + - - +
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Residues in contact with VAL 149 (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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34A VAL* 4.6 5.6 - - + -
144A SER* 3.6 17.0 - - - +
146A LEU* 3.1 21.3 + - + +
148A GLU* 1.3 74.9 - - - +
150A ALA* 1.3 66.5 + - - +
152A ARG* 3.2 25.7 + - - +
153A PHE* 3.3 20.6 - - + -
188A LYS* 3.6 34.3 - - + -
189A GLU* 3.7 37.9 - - + +
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Residues in contact with ALA 150 (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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116A TYR* 3.6 46.0 - - + +
117A ARG* 3.7 10.5 - - - +
118A GLY* 3.9 11.1 + - - +
144A SER* 4.6 2.4 - - - -
146A LEU 3.4 2.6 + - - +
147A PRO* 3.2 6.8 + - + +
149A VAL* 1.3 80.9 - - - +
151A LYS* 1.3 62.5 + - + +
152A ARG 3.3 0.5 + - - -
153A PHE* 3.4 13.5 + - - +
154A SER* 3.7 9.2 + - - -
168A LEU* 5.1 3.4 - - + -
188A LYS* 5.8 3.1 - - - +
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Residues in contact with LYS 151 (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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23A ALA 5.1 0.9 + - - -
24A ILE* 3.2 38.2 + - + +
26A GLN 3.3 15.0 + - - -
27A PRO* 5.1 0.2 - - - +
28A ASN* 2.9 33.0 + - - +
147A PRO* 3.0 26.7 + - + +
148A GLU 3.7 4.9 - - - +
149A VAL 3.3 0.2 - - - -
150A ALA* 1.3 78.1 - - + +
152A ARG* 1.3 64.5 + - - +
153A PHE 3.2 0.9 + - - -
154A SER* 3.5 1.7 + - - -
155A VAL* 3.7 4.6 - - - +
166A ARG* 2.5 34.0 + - - +
168A LEU* 4.2 21.3 - - + -
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Residues in contact with ARG 152 (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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28A ASN* 6.3 0.2 - - - +
31A GLU* 6.2 3.8 - - - +
34A VAL* 4.4 18.2 - - - +
148A GLU* 3.3 19.8 + - - +
149A VAL* 3.4 19.8 - - - +
150A ALA 3.1 0.8 - - - -
151A LYS* 1.3 79.9 - - - +
153A PHE* 1.3 72.8 + - + +
154A SER 3.3 1.3 + - - -
155A VAL* 3.7 17.4 + - - +
189A GLU* 3.3 35.6 + - - -
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Residues in contact with PHE 153 (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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72A TYR* 5.1 12.8 - + - -
118A GLY 5.0 6.8 - - - +
120A TRP* 5.1 2.1 + - - -
149A VAL* 3.3 29.2 - - + -
150A ALA* 3.4 9.6 + - - +
151A LYS 3.2 1.2 - - - -
152A ARG* 1.3 91.6 - - + +
154A SER* 1.3 60.0 + - - +
155A VAL 3.7 0.9 - - - -
188A LYS* 4.1 40.2 - - + -
189A GLU* 5.9 0.4 - - - -
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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