Contacts of the helix formed by residues 114 - 118 (chain A) in PDB entry 5J2Q
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 ALA 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.3 8.6 + - - +
112A GLY 3.5 1.2 - - - -
113A ASP* 1.3 77.2 - - - +
115A TYR* 1.3 66.1 + - - +
117A SER* 3.1 11.6 + - - -
118A VAL* 3.8 4.0 - - - +
160A PHE* 3.6 32.9 - - + -
185A ASP* 3.8 16.4 + - + +
214A LEU* 5.5 0.2 - - - -
801T 6FM 3.4 38.3 + - + +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ALA* 1.3 78.8 - - - +
116A PHE* 1.3 65.0 + - + +
117A SER 3.0 6.1 + - - -
118A VAL* 3.2 11.3 + - - +
149A LEU* 3.3 39.5 + - + +
150A PRO 3.9 8.7 - - - -
151A GLN* 3.5 26.0 - - + +
152A GLY 5.4 0.2 - - - -
156A SER* 3.7 31.9 - - - -
157A PRO* 3.2 31.2 - - + +
160A PHE* 3.8 17.0 - + + -
184A MET* 4.7 2.6 - - - -
901P 6FM 4.4 5.0 - - - -
801T 6FM 3.2 66.6 + + + +
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Residues in contact with PHE 116 (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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1A PRO 4.1 0.7 - - - +
2A ILE* 4.7 0.2 - - - +
37A ILE* 5.5 2.9 - - + -
41A MET* 4.0 24.7 - - + -
46A LYS* 3.3 41.6 - - + +
73A LYS* 4.5 15.9 - - + -
113A ASP* 3.8 23.9 + - + -
114A ALA 3.2 1.4 - - - -
115A TYR* 1.3 75.2 - - + +
117A SER* 1.3 58.9 + - - +
118A VAL 3.7 0.4 - - - -
146A TYR* 3.9 24.5 - + - -
148A VAL* 3.7 23.6 - - + +
149A LEU 3.4 20.4 - - - -
150A PRO* 4.3 0.7 - - + -
151A GLN* 3.8 38.1 - - + -
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Residues in contact with SER 117 (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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1A PRO 3.4 21.4 + - - -
2A ILE* 3.5 3.5 - - - +
3A SER* 2.6 35.4 + - - -
46A LYS* 5.1 0.9 + - - -
112A GLY 3.9 6.4 + - - -
113A ASP* 2.6 26.7 + - - +
114A ALA 3.1 4.5 + - - -
115A TYR 3.0 1.6 + - - -
116A PHE* 1.3 78.3 - - - +
118A VAL* 1.3 59.3 + - - +
148A VAL* 4.7 0.2 - - - -
213A GLY 3.7 16.5 + - - -
214A LEU* 4.0 12.2 - - - +
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Residues in contact with VAL 118 (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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3A SER* 4.5 4.5 - - - -
5A ILE* 4.6 4.9 - - + -
6A GLU 6.0 0.4 - - - +
114A ALA 3.8 5.4 - - - +
115A TYR 3.2 2.3 + - - +
117A SER* 1.3 81.5 - - - +
119A PRO* 1.3 80.3 - - + +
148A VAL* 3.3 4.7 - - - -
149A LEU* 3.1 45.3 + - + +
159A ILE* 4.7 2.5 - - + -
160A PHE* 3.7 31.9 - - + -
163A SER* 3.9 28.7 - - - +
167A ILE* 5.8 3.6 - - + -
214A LEU* 5.0 6.5 - - + -
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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