Contacts of the helix formed by residues 114 - 120 (chain B) in PDB entry 2Y05
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PHE* 5.8 3.6 - - + -
109B TRP* 3.4 10.3 - - - -
112B THR 4.2 1.3 - - - +
113B ILE* 1.3 89.0 - - + +
115B LEU* 1.3 63.5 + - - +
116B SER* 3.4 21.1 - - - +
117B LEU* 3.1 19.3 + - + +
298B TYR* 3.3 28.3 - - + +
300B GLU* 3.6 15.9 - - - +
289C LYS* 3.7 26.2 - - + +
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Residues in contact with LEU 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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42B LEU* 4.2 24.7 - - + -
43B PHE* 4.3 15.4 - - + -
68B VAL* 3.5 19.0 - - + +
84B ILE* 4.3 21.3 - - + -
105B LEU* 3.9 22.1 - - + +
109B TRP* 4.0 19.7 - - + +
113B ILE 3.4 3.1 + - - +
114B PRO* 1.3 71.0 - - - +
116B SER* 1.3 55.8 + - - +
117B LEU 3.2 0.4 - - - -
118B ALA* 3.1 29.6 + - - +
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Residues in contact with SER 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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43B PHE* 3.7 41.5 - - - -
68B VAL* 4.5 4.0 - - - -
114B PRO* 3.4 9.2 - - - +
115B LEU* 1.3 74.3 - - - +
117B LEU* 1.3 60.5 + - - +
118B ALA 3.0 5.2 - - - -
119B LEU* 3.0 20.5 + - - +
120B GLY* 3.8 2.6 + - - -
300B GLU* 2.4 37.5 + - - +
302B ILE* 5.5 0.9 - - - +
324B LYS* 5.5 0.5 - - - +
326B ILE* 4.0 16.1 - - - +
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Residues in contact with LEU 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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109B TRP* 3.9 13.2 - - + -
113B ILE* 4.5 8.5 - - + -
114B PRO* 3.1 23.6 + - + +
116B SER* 1.3 77.2 + - - +
118B ALA* 1.3 55.2 + - - +
119B LEU 3.1 1.1 - - - -
120B GLY* 3.0 13.0 + - - +
121B THR* 4.7 10.5 - - - +
122B VAL* 2.8 41.5 + - + +
291B VAL* 4.4 13.9 - - + -
298B TYR* 3.7 49.4 - - + -
300B GLU* 3.7 28.0 - - + +
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Residues in contact with ALA 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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66B GLN* 4.5 2.1 - - - +
68B VAL* 4.1 1.8 - - + -
86B LEU* 3.6 28.4 - - + +
105B LEU* 3.8 28.5 - - + -
109B TRP* 3.5 14.5 - - + -
115B LEU 3.1 15.9 + - - +
116B SER 3.0 1.4 - - - -
117B LEU* 1.3 75.9 - - - +
119B LEU* 1.3 58.0 + - - +
120B GLY 3.5 0.2 - - - -
122B VAL 3.4 13.0 - - - +
123B GLY* 3.5 14.0 - - - -
124B MET 4.5 1.2 + - - -
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Residues in contact with LEU 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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43B PHE* 3.5 35.7 - - + +
44B LEU 3.9 15.3 - - - -
45B THR* 3.9 14.2 + - + +
47B ASP* 5.1 0.2 - - - +
66B GLN* 3.7 31.6 - - + +
67B GLN* 4.0 8.5 - - - +
68B VAL* 3.8 14.6 - - + +
86B LEU* 3.7 17.3 - - + -
116B SER 3.0 9.9 + - - +
118B ALA* 1.3 78.9 - - - +
120B GLY* 1.3 54.3 + - - +
124B MET* 4.7 1.3 - - - +
125B PRO* 3.3 14.7 - - - +
324B LYS* 3.2 20.3 - - - -
326B ILE* 3.9 17.9 - - + -
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Residues in contact with GLY 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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116B SER 3.8 1.5 + - - -
117B LEU* 3.0 8.5 + - - -
118B ALA 3.5 1.0 - - - -
119B LEU* 1.3 79.7 - - - +
121B THR* 1.3 66.8 + - - -
122B VAL 3.2 1.3 - - - -
123B GLY* 3.0 13.0 + - - +
125B PRO* 3.6 8.0 - - - +
126B GLY 3.1 17.3 + - - -
153B ALA* 5.5 1.3 - - - -
324B LYS* 4.0 21.1 - - - -
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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