Contacts of the helix formed by residues 112 - 125 (chain B) 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 ASP 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ASP 4.2 0.6 + - - -
111B ARG* 1.3 70.7 - - - +
113B PRO* 1.4 73.5 - - - +
114B VAL* 3.3 18.3 + - - +
115B PRO* 3.3 32.3 - - + +
116B LEU* 3.6 15.1 - - - +
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Residues in contact with PRO 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 4.7 4.3 - - + -
101B ALA* 4.6 8.3 - - + -
104B VAL* 4.1 26.0 - - + -
105B LYS* 4.0 33.0 - - + -
109B PRO 5.8 0.7 - - - +
111B ARG 3.1 10.5 - - - +
112B ASP* 1.4 88.1 - - - +
114B VAL* 1.3 62.7 + - + +
116B LEU* 2.9 4.8 + - + +
117B VAL* 2.7 38.5 + - + +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.2 22.4 - - + -
112B ASP* 3.8 9.9 - - - +
113B PRO* 1.3 82.5 - - + +
115B PRO* 1.3 68.5 - - + +
117B VAL* 3.7 2.1 - - - +
118B LYS* 3.0 57.5 + - - +
128B PHE* 4.4 11.2 - - + -
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Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASP* 3.3 35.9 - - + +
114B VAL* 1.3 96.8 - - + +
116B LEU* 1.3 60.7 + - + -
118B LYS* 3.9 10.4 - - + +
119B LYS* 3.0 31.0 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.2 20.4 - - + -
108B TYR* 6.0 1.3 - - + -
111B ARG* 4.3 25.1 - - + +
112B ASP 3.6 18.8 - - - +
113B PRO* 2.9 8.0 + - + +
115B PRO* 1.3 79.7 - - + +
117B VAL* 1.3 58.6 + - - +
119B LYS* 3.4 12.4 + - - +
120B ALA* 3.0 29.5 + - - +
154B VAL* 3.6 26.6 - - + +
155B HIS* 5.7 0.7 - - - -
156B GLU* 3.3 35.0 - - + +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B PHE* 3.8 26.2 - - + +
100B VAL* 4.0 13.7 - - + -
101B ALA* 3.6 37.9 - - + +
104B VAL* 4.8 0.2 - - + -
113B PRO* 2.7 23.1 + - + +
114B VAL 3.7 3.6 - - - +
116B LEU* 1.3 73.9 - - - +
118B LYS* 1.3 66.1 + - - +
119B LYS 3.0 1.3 - - - -
120B ALA* 3.0 2.9 + - - +
121B MET* 2.7 52.2 + - - +
128B PHE* 4.1 2.0 - - + -
154B VAL* 4.1 11.4 - - + -
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B VAL* 3.0 36.8 + - + +
115B PRO* 3.9 9.2 - - + +
117B VAL* 1.3 74.9 - - - +
119B LYS* 1.3 65.8 + - + +
121B MET* 3.1 1.6 + - - +
122B GLU* 2.9 31.7 + - + +
128B PHE* 3.3 57.2 - - + -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO 3.0 16.4 + - - +
116B LEU* 3.9 13.4 + - - +
117B VAL 3.0 1.0 - - - -
118B LYS* 1.3 82.3 - - + +
120B ALA* 1.3 57.8 + - - +
122B GLU* 3.9 4.6 - - - +
123B PHE* 3.0 31.2 + - + +
154B VAL 5.6 0.2 + - - -
156B GLU* 3.0 41.2 + - - +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 4.2 2.9 - - + -
116B LEU 3.0 17.8 + - - +
117B VAL 3.7 3.1 - - - +
119B LYS* 1.3 73.2 - - - +
121B MET* 1.3 64.5 + - - +
123B PHE* 3.5 3.3 + - - +
124B VAL* 3.3 25.1 + - - +
150B ALA* 3.6 32.4 - - + +
153B ILE* 4.3 12.7 - - + +
154B VAL* 3.8 18.6 - - + +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 3.6 30.7 - - + -
97B PHE* 5.2 1.1 - - - -
100B VAL* 4.4 14.8 - - + -
117B VAL* 2.7 44.4 + - + +
118B LYS* 3.8 4.5 - - - +
120B ALA* 1.3 73.6 - - - +
122B GLU* 1.3 56.4 + - - +
124B VAL* 3.4 9.1 - - - +
125B GLY 3.1 4.7 + - - -
126B LEU* 2.7 57.4 + - + +
128B PHE* 3.9 21.5 - - + +
131B PHE* 3.7 22.9 - - + -
132B LYS* 3.8 14.6 - - - +
150B ALA* 4.5 2.2 - - + -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LYS* 2.9 24.3 + - + +
119B LYS* 3.9 5.8 - - - +
121B MET* 1.3 73.3 - - - +
123B PHE* 1.3 65.1 + - - +
124B VAL 3.1 2.0 - - - -
125B GLY* 3.1 14.5 + - - +
126B LEU 3.5 6.0 - - - +
127B ASP* 3.6 12.4 - - - +
128B PHE* 3.0 35.2 + - - +
183B LYS* 4.7 2.9 + - - -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 3.0 20.3 + - + +
120B ALA* 3.7 6.1 - - - +
122B GLU* 1.3 77.4 - - - +
124B VAL* 1.3 60.6 + - - +
125B GLY* 3.6 0.3 + - - -
153B ILE* 3.4 22.2 - - + -
179B ARG* 5.1 1.0 + - - -
180B ILE* 4.1 26.9 - - + +
183B LYS* 3.1 61.9 + - + +
184B TRP* 3.5 46.2 - + - -
187B LEU* 3.9 25.4 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA 3.3 11.1 + - - +
121B MET 3.4 13.7 - - - +
122B GLU 3.1 0.4 - - - -
123B PHE* 1.3 80.1 - - - +
125B GLY* 1.3 57.6 + - - +
126B LEU* 3.7 21.8 - - + -
146B ARG* 3.3 47.2 - - + +
149B ILE* 3.7 27.1 - - + -
150B ALA* 3.9 8.5 - - + +
153B ILE* 4.8 3.8 - - + -
179B ARG* 3.6 16.8 + - - -
180B ILE* 3.9 20.3 - - + +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B GLU* 3.1 14.3 + - - -
123B PHE 3.3 0.6 - - - -
124B VAL* 1.3 78.9 - - - +
126B LEU* 1.3 63.2 + - - +
127B ASP 4.1 1.7 + - - -
131B PHE* 5.5 1.2 - - - -
146B ARG* 2.7 26.9 + - - -
179B ARG* 5.0 3.8 - - - -
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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