Contacts of the helix formed by residues 89 - 93 (chain A) in PDB entry 2J9R
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 GLU 89 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 6.1 2.0 - - - -
22A SER* 4.9 3.8 + - - -
43A LYS* 6.0 2.0 - - + -
44A PRO* 3.8 15.0 - - + +
88A ASP* 1.3 96.5 + - + +
90A VAL* 1.3 61.2 + - - +
91A GLN* 3.0 40.5 + - - +
92A PHE* 3.1 32.8 + - + +
93A PHE* 3.8 3.8 - - - -
114A ALA 2.8 8.9 + - - -
115A GLY* 4.4 0.7 - - - -
1195A THM 3.0 31.3 + - - -
1196A PO4 5.6 1.9 + - - -
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Residues in contact with VAL 90 (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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12A VAL* 6.2 1.1 - - + -
87A ILE* 3.5 32.3 - - + +
88A ASP 3.2 0.8 + - - -
89A GLU* 1.3 69.6 - - - +
91A GLN* 1.3 65.2 + - - +
92A PHE 2.9 3.1 - - - -
93A PHE* 2.8 28.2 + - + +
97A ILE* 4.6 11.1 - - + +
113A VAL* 3.5 32.1 - - + -
114A ALA 2.9 24.8 + - - +
115A GLY* 3.4 7.0 - - - +
127A GLN* 5.3 2.6 + - - +
128A VAL* 4.0 12.6 - - + -
131A LEU* 4.1 13.1 - - + +
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Residues in contact with GLN 91 (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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21A LYS* 5.6 0.8 - - - +
89A GLU* 3.0 52.0 + - - +
90A VAL* 1.3 75.9 - - - +
92A PHE* 1.3 85.8 + - - +
93A PHE 3.5 5.7 + - - +
115A GLY* 3.2 13.9 - - - -
116A LEU* 3.1 46.8 - - + +
125A PHE* 3.5 35.1 - - + -
126A GLY* 4.0 15.6 - - - -
127A GLN 5.1 0.7 - - - +
128A VAL* 3.7 10.2 - - + +
171A ILE* 5.7 1.4 - - - +
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Residues in contact with PHE 92 (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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44A PRO* 3.7 22.9 - - + +
89A GLU* 3.1 28.1 + - + +
90A VAL 2.8 1.2 + - - -
91A GLN* 1.3 96.5 - - + +
93A PHE* 1.3 63.5 + - - +
94A ASP* 3.7 1.4 + - - -
125A PHE* 4.3 5.4 - + - -
171A ILE* 4.2 30.9 - - + +
173A VAL* 4.5 14.8 - - + -
1195A THM 3.1 56.1 - + - -
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Residues in contact with PHE 93 (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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42A PHE* 4.6 0.7 - - + -
43A LYS* 3.6 23.1 - - - -
44A PRO* 3.6 18.6 - - + -
68A VAL* 3.5 25.8 - - + -
70A ALA 4.9 0.9 - - - -
71A SER* 3.6 26.5 - - - +
74A ILE* 4.2 10.3 - - + -
87A ILE* 3.5 29.6 - - + -
88A ASP 3.5 13.7 - - - -
89A GLU 3.8 2.7 - - - -
90A VAL* 2.8 28.8 + - - +
91A GLN 4.0 6.1 - - - +
92A PHE* 1.3 80.2 - - - +
94A ASP* 1.3 64.6 + - - +
97A ILE* 3.7 23.3 - - + -
126A GLY* 5.7 0.5 - - - -
127A GLN* 4.3 9.9 + - - +
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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