Contacts of the helix formed by residues 115 - 120 (chain A) in PDB entry 2UYQ
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 SER 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG* 5.5 0.2 - - - -
38A ASP* 2.7 34.3 + - - -
40A TYR* 3.7 23.9 - - - -
44A LEU* 4.9 4.7 - - - -
113A LEU 3.2 6.4 + - - -
114A ASP* 1.3 73.0 + - - +
116A ARG* 1.3 65.8 + - - +
117A ALA 3.1 3.6 - - - -
118A TYR* 2.8 25.9 + - - +
119A ARG* 2.9 22.9 + - - +
140A LYS* 5.3 0.7 - - - -
144A LEU* 5.8 0.9 - - - -
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Residues in contact with ARG 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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25A ARG* 6.1 0.8 - - - +
88A THR* 3.3 31.1 + - - +
91A PHE* 3.5 19.4 - - - +
92A ASP* 2.7 30.3 + - - +
95A PHE* 3.8 27.8 - - + -
108A ILE* 4.1 8.3 - - + -
114A ASP* 2.8 42.9 + - - +
115A SER* 1.3 76.9 - - - +
117A ALA* 1.3 62.5 + - - +
118A TYR 3.1 1.4 + - - -
119A ARG* 3.6 22.5 - - - +
120A LEU* 3.2 27.2 + - + +
122A TRP* 3.1 17.2 + - + -
184A LEU* 3.5 7.3 - - - +
186A GLU* 2.9 25.0 + - - -
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Residues in contact with ALA 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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108A ILE* 4.5 4.6 - - + +
114A ASP 5.1 0.2 + - - -
115A SER 3.0 1.2 + - - -
116A ARG* 1.3 76.9 - - - +
118A TYR* 1.3 59.6 + - + +
122A TRP* 3.5 23.2 + - - +
128A VAL* 4.0 19.1 - - + -
130A GLU* 3.4 23.7 + - - +
151A PRO* 4.0 7.4 - - - +
152A THR 5.2 0.2 + - - -
153A ALA* 4.0 12.3 + - - +
155A ARG* 3.6 26.9 - - + -
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Residues in contact with TYR 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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40A TYR* 3.7 27.3 + + + +
115A SER* 2.8 19.4 + - - +
117A ALA* 1.3 82.9 - - + +
119A ARG* 1.3 63.6 + - - +
120A LEU 3.7 5.7 - - - +
130A GLU* 4.4 4.0 - - - -
140A LYS* 4.8 7.5 - - - +
141A SER* 4.7 9.5 - - - -
144A LEU* 3.4 31.2 - - + +
149A VAL* 3.8 18.8 - - + -
150A THR* 3.9 5.6 - - - -
151A PRO* 3.6 41.0 - - + +
152A THR* 5.5 3.5 + - - +
155A ARG* 3.4 46.8 + - - -
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Residues in contact with ARG 119 (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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25A ARG* 5.0 3.4 - - - +
36A ILE* 5.4 1.8 - - - +
37A ARG 3.9 12.1 + - - +
38A ASP* 3.6 32.5 + - - +
39A PRO* 4.0 7.9 - - + -
40A TYR* 3.7 19.3 - - + -
88A THR* 3.5 17.9 - - - +
92A ASP* 2.8 43.6 + - - -
114A ASP* 4.5 2.8 + - - -
115A SER* 2.9 34.5 + - - +
116A ARG* 3.6 22.2 - - - +
118A TYR* 1.3 79.0 - - - +
120A LEU* 1.3 77.0 + - - +
121A ASP* 3.9 3.5 + - - +
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Residues in contact with LEU 120 (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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92A ASP* 4.1 16.6 - - + +
95A PHE* 3.9 24.7 - - + -
96A ASN* 4.0 22.2 - - - +
116A ARG* 3.2 38.9 + - + +
118A TYR 4.2 5.0 - - - +
119A ARG* 1.3 107.5 - - - +
121A ASP* 1.3 62.4 + - - +
122A TRP* 3.2 40.1 + - + -
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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