Contacts of the helix formed by residues 111 - 124 (chain A) in PDB entry 1Y24
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 PHE 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 4.6 0.9 - - - -
108A SER 5.6 0.4 - - - -
109A TYR* 3.5 25.0 + + - +
110A ASN* 1.3 121.1 - - - +
112A THR* 1.3 57.1 + - - +
113A HIS 3.4 2.0 - - - -
114A LEU* 3.1 11.2 + - + +
115A ASP* 2.8 55.7 + - - +
158A SER* 3.8 19.3 - - - -
159A LEU* 3.8 26.7 - - + -
162A ARG* 3.4 46.7 - - + -
163A TYR* 5.9 2.0 - + - -
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Residues in contact with THR 112 (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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98A THR 5.7 0.2 + - - -
109A TYR* 3.7 22.4 + - - -
110A ASN 3.9 0.8 - - - -
111A PHE* 1.3 73.6 - - - +
113A HIS* 1.3 78.3 + - + +
115A ASP* 3.4 8.1 + - - +
116A GLY* 3.2 17.2 + - - -
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Residues in contact with HIS 113 (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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97A VAL 4.5 7.2 + - - -
98A THR* 3.2 45.5 + - + +
99A THR* 4.6 10.4 + - - -
111A PHE 3.4 0.4 - - - -
112A THR* 1.3 91.6 - - + +
114A LEU* 1.3 58.3 + - - +
116A GLY* 3.4 1.6 + - - -
117A TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 114 (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 TRP* 4.3 15.7 - - + -
93A LEU* 3.8 19.3 - - + -
98A THR* 4.4 7.1 + - + -
100A ARG* 3.1 39.7 - - + +
110A ASN 5.5 0.2 - - - +
111A PHE* 3.1 14.7 + - + +
113A HIS* 1.3 74.9 - - - +
115A ASP* 1.3 61.3 + - - +
117A TYR* 3.2 10.8 + - + -
118A LEU* 2.8 44.5 + - + +
159A LEU* 3.7 14.1 - - + -
163A TYR* 3.4 31.2 - - + +
167A TYR* 4.5 0.4 - - - -
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TYR* 2.8 25.1 + - - -
111A PHE* 2.8 40.2 + - - +
112A THR* 3.6 7.4 + - - +
114A LEU* 1.3 70.4 - - - +
116A GLY* 1.3 58.2 + - - +
119A ASP* 2.7 40.0 + - - +
162A ARG* 3.9 7.4 + - - +
166A ARG* 3.5 40.1 + - - +
167A TYR* 3.3 9.0 + - - -
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Residues in contact with GLY 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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112A THR 3.2 10.6 + - - -
113A HIS 3.7 3.1 - - - -
115A ASP* 1.3 78.5 - - - +
117A TYR* 1.3 62.1 + - - +
119A ASP* 3.4 5.6 - - - +
120A LEU* 3.0 25.1 + - - +
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Residues in contact with TYR 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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56A LEU* 3.6 24.3 - - + +
66A LEU* 5.3 10.8 - - + -
88A VAL* 4.4 1.4 - - - +
90A THR* 3.7 14.9 - - + +
92A TRP* 3.4 43.6 - + + -
93A LEU* 5.3 4.3 - - + -
113A HIS 2.9 18.4 + - - +
114A LEU* 3.2 12.1 + - + +
116A GLY* 1.3 72.6 - - - +
118A LEU* 1.3 75.4 + - + +
120A LEU* 3.1 13.5 + - + +
121A LEU* 3.0 63.2 + - + +
128A PRO* 5.7 0.4 - - + -
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Residues in contact with LEU 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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93A LEU* 5.5 5.2 - - + -
114A LEU* 2.8 25.5 + - + +
117A TYR* 1.3 93.2 - - + +
119A ASP* 1.3 64.1 + - - +
121A LEU* 3.2 6.8 + - + +
122A ARG* 2.9 32.7 + - - +
128A PRO* 3.6 30.7 - - + -
163A TYR* 3.4 35.0 - - + +
167A TYR* 3.3 28.7 - - + +
175A TRP* 3.8 13.9 - - + -
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Residues in contact with ASP 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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115A ASP 2.7 29.1 + - - +
116A GLY* 3.4 6.4 - - - +
118A LEU* 1.3 76.6 - - - +
120A LEU* 1.3 50.4 + - - +
122A ARG* 3.2 26.6 + - - +
123A GLU* 2.8 40.8 + - - +
166A ARG* 3.1 23.4 + - - -
167A TYR* 2.8 21.1 + - - -
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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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66A LEU* 5.9 4.3 - - + -
67A SER* 3.6 30.7 - - - -
70A GLN* 4.4 5.4 - - - +
71A GLN* 5.3 4.0 - - - +
116A GLY 3.0 13.0 + - - +
117A TYR* 3.3 15.7 - - + +
119A ASP* 1.3 75.6 - - - +
121A LEU* 1.3 59.5 + - + +
123A GLU* 3.3 23.2 + - - +
124A ASN* 2.9 55.6 + - - +
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Residues in contact with LEU 121 (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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56A LEU* 4.2 2.5 - - + -
66A LEU* 6.3 0.4 - - + -
70A GLN* 3.7 31.6 - - - +
88A VAL* 3.7 23.3 - - + -
117A TYR* 3.0 64.8 + - + +
118A LEU* 3.2 23.1 + - + +
120A LEU* 1.3 76.2 - - + +
122A ARG* 1.3 60.3 + - - +
124A ASN* 3.2 12.1 + - - +
125A GLN 3.4 0.3 + - - -
126A LEU* 3.0 33.8 + - - +
128A PRO* 4.1 15.7 - - + -
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Residues in contact with ARG 122 (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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118A LEU* 2.9 18.7 + - - +
119A ASP* 3.2 35.5 + - - +
121A LEU* 1.3 71.3 - - - +
123A GLU* 1.3 59.7 + - - +
125A GLN* 2.9 22.0 + - - -
126A LEU 3.7 12.3 - - - +
128A PRO* 4.9 6.3 - - + -
166A ARG* 5.5 0.6 - - - +
167A TYR* 3.1 36.3 - - - +
171A HIS* 3.4 39.6 + - + +
175A TRP* 4.7 2.5 - - - -
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Residues in contact with GLU 123 (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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71A GLN* 4.8 6.2 + - - -
119A ASP* 2.8 22.9 + - - +
120A LEU* 3.3 28.9 + - - +
122A ARG* 1.3 72.5 - - - +
124A ASN* 1.3 63.8 + - - +
125A GLN* 3.2 4.7 + - - +
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Residues in contact with ASN 124 (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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67A SER 4.4 1.4 + - - -
70A GLN* 2.9 28.4 + - + +
71A GLN* 3.1 46.9 + - - +
74A LEU* 3.0 34.1 - - + +
120A LEU* 2.9 34.0 + - - +
121A LEU 3.2 5.8 + - - +
123A GLU* 1.3 78.6 - - - +
125A GLN* 1.3 63.6 + - - +
126A LEU 3.5 0.9 - - - -
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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