Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 2YZ2
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 PRO 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 4.4 14.8 - - + -
101A ALA* 4.2 17.5 - - + -
104A VAL* 3.9 35.4 - - + -
105A LYS* 4.3 15.5 - - + +
111A ARG* 3.2 7.4 - - + +
112A ASP* 1.3 89.8 - - + +
114A VAL* 1.3 65.5 + - + +
115A PRO* 3.4 0.9 - - - -
116A LEU* 3.2 6.3 + - + +
117A VAL* 2.9 23.6 + - + +
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Residues in contact with VAL 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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97A PHE* 3.6 27.3 - - + -
112A ASP* 3.0 21.0 + - - +
113A PRO* 1.3 77.5 - - + +
115A PRO* 1.4 67.0 - - + +
117A VAL* 3.1 2.3 + - - +
118A LYS* 2.8 35.4 + - + +
128A PHE* 4.2 21.3 - - + -
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Residues in contact with PRO 115 (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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111A ARG* 6.2 2.0 - - + -
112A ASP* 3.1 26.5 - - - +
113A PRO 3.5 0.9 - - - -
114A VAL* 1.4 98.2 - - + +
116A LEU* 1.3 64.2 + - + +
118A LYS* 3.8 5.8 - - + +
119A LYS* 3.0 41.5 + - - +
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Residues in contact with LEU 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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104A VAL* 4.2 15.7 - - + -
108A TYR* 4.2 31.6 - - + -
111A ARG* 4.6 22.0 - - - +
113A PRO* 3.2 7.4 + - + +
115A PRO* 1.3 82.4 - - + +
117A VAL* 1.3 64.9 + - - +
119A LYS* 3.2 13.0 + - + +
120A ALA* 2.9 24.1 + - - +
154A VAL* 3.6 30.4 - - + +
155A HIS* 5.0 2.2 - - - -
156A GLU* 3.6 28.5 - - + +
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Residues in contact with VAL 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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97A PHE* 3.4 32.5 - - + +
100A VAL* 4.0 14.1 - - + -
101A ALA* 3.5 39.5 - - + +
104A VAL* 4.1 8.1 - - + -
113A PRO 2.9 22.1 + - - +
114A VAL 3.7 2.9 - - - +
116A LEU* 1.3 74.8 - - - +
118A LYS* 1.3 57.5 + - - +
120A ALA* 3.1 4.0 + - - +
121A MET* 2.8 49.0 + - + +
128A PHE* 4.3 0.7 - - + -
154A VAL* 4.1 5.2 - - - -
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Residues in contact with LYS 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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114A VAL* 2.8 22.6 + - + +
115A PRO* 3.8 6.3 - - + +
117A VAL* 1.3 78.1 - - - +
119A LYS* 1.3 57.7 + - + +
121A MET* 3.9 0.6 - - - +
122A GLU* 2.9 53.1 + - + +
128A PHE* 3.7 49.1 - - + +
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Residues in contact with LYS 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 PRO* 3.0 34.5 + - - +
116A LEU* 3.2 12.8 + - + +
118A LYS* 1.3 75.5 - - + +
120A ALA* 1.3 55.4 + - - +
122A GLU* 4.1 4.4 - - - +
123A PHE* 2.7 36.4 + - - +
156A GLU* 4.6 16.6 - - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.1 5.4 - - + -
116A LEU 2.9 13.2 + - - +
117A VAL 3.5 7.0 - - - +
119A LYS* 1.3 73.8 - - - +
121A MET* 1.3 65.1 + - - +
123A PHE* 3.1 17.7 + - - +
124A VAL* 3.1 17.5 + - - +
150A ALA* 3.5 28.3 - - + +
153A ILE* 4.5 5.4 - - + -
154A VAL* 3.7 21.8 - - + +
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Residues in contact with MET 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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96A VAL* 3.9 18.8 - - + -
97A PHE* 4.9 2.5 - - - -
100A VAL* 4.6 13.5 - - + -
117A VAL* 2.8 44.1 + - + +
118A LYS* 3.9 4.9 - - - +
120A ALA* 1.3 71.8 - - - +
122A GLU* 1.3 65.2 + - - +
124A VAL* 3.3 10.2 + - - +
125A GLY 3.1 4.7 + - - -
126A LEU* 2.9 37.2 + - + +
128A PHE* 3.8 39.9 - - - +
131A PHE* 3.8 24.5 - - + -
132A LYS* 3.9 10.1 - - - +
150A ALA* 4.4 2.2 - - + -
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Residues in contact with GLU 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 LYS* 2.9 45.1 + - + +
119A LYS* 4.1 4.9 - - - +
121A MET* 1.3 75.4 - - - +
123A PHE* 1.4 57.2 + - - +
125A GLY* 2.9 19.9 + - - -
126A LEU 4.0 2.5 - - - +
127A ASP* 3.7 19.9 + - - +
128A PHE* 2.9 36.7 + - + +
183A LYS* 3.7 8.1 + - - -
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Residues in contact with PHE 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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119A LYS 2.7 22.9 + - - +
120A ALA* 3.1 8.5 + - - +
122A GLU* 1.4 70.9 - - - +
124A VAL* 1.3 57.9 + - - +
125A GLY 3.1 1.4 + - - -
153A ILE* 3.9 22.2 - - + -
180A ILE* 3.9 32.0 - - + +
183A LYS* 3.1 44.9 + - + +
184A TRP* 3.6 48.0 - + - -
187A LEU* 3.4 25.4 - - + -
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Residues in contact with VAL 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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120A ALA 3.1 14.6 + - - +
121A MET 3.5 11.4 - - - +
123A PHE* 1.3 76.4 - - - +
125A GLY* 1.3 56.4 + - - +
126A LEU* 3.7 18.6 - - + -
146A ARG* 2.9 49.9 + - + +
149A ILE* 3.9 16.6 - - + -
150A ALA* 3.7 28.7 - - + +
153A ILE* 3.9 9.0 - - + -
180A ILE* 3.7 23.2 - - + +
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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