Contacts of the strand formed by residues 115 - 119 (chain C) in PDB entry 1O97
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 MET 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LYS 3.6 3.0 + - - -
3C ILE* 3.7 11.5 - - + -
4C LEU 3.1 23.6 + - - -
113C PRO* 3.5 4.2 - - - +
114C ASP* 1.3 89.2 - - + +
116C VAL* 1.3 67.5 + - - +
117C PHE* 4.0 19.5 - - + -
140C TRP* 4.4 1.8 - - - -
149C LEU* 5.0 1.1 - - + -
151C TYR* 3.7 36.1 - - + +
158C ALA* 4.9 3.8 - - + -
174C ILE* 5.9 0.2 - - + -
176C CYS* 3.6 34.5 - - - -
178C ALA* 3.7 25.1 - - + +
180C LEU* 4.1 26.7 - - + -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.3 14.4 - - + +
6C ALA* 5.4 4.0 - - + +
108C ILE* 4.1 33.4 - - + -
113C PRO* 3.8 16.8 - - + -
115C MET* 1.3 80.3 - - - +
117C PHE* 1.3 75.3 + - - +
118C ALA* 5.6 1.6 - - + -
134C VAL* 4.7 4.0 - - + -
138C LEU* 4.6 1.6 - - + -
140C TRP* 3.7 17.5 - - + -
178C ALA 3.1 5.9 + - - +
179C VAL* 3.3 26.5 - - + +
180C LEU 3.0 26.0 + - - -
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ILE* 3.9 16.8 - - + -
4C LEU 3.0 9.3 + - - +
5C VAL* 3.4 8.1 - - + +
6C ALA* 3.0 27.7 + - - +
42C SER* 3.6 25.1 - - - -
45C GLU* 4.0 9.9 - - + -
46C ALA* 3.7 28.5 - - + -
49C ILE* 3.7 11.0 - - + -
115C MET* 4.0 20.8 - - + -
116C VAL* 1.3 85.5 - - - +
118C ALA* 1.3 60.5 + - - +
149C LEU* 3.7 23.1 - - + -
180C LEU* 3.5 30.1 - - + -
182C ILE* 4.1 17.0 - - + -
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ALA* 4.2 6.7 - - + -
42C SER* 4.7 5.2 - - - -
116C VAL* 4.3 2.4 + - + +
117C PHE* 1.3 74.6 - - - +
119C GLY* 1.4 66.2 + - - +
131C GLY* 3.7 30.5 - - - +
134C VAL* 6.4 0.2 - - + -
179C VAL* 5.2 3.6 - - + -
180C LEU 3.0 9.3 + - - +
181C THR* 3.1 4.3 - - + -
182C ILE* 2.8 26.5 + - - +
1262C AMP 3.2 17.5 - - - +
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TRP* 3.8 18.8 - - - -
39C ASP* 3.7 5.4 + - - -
42C SER* 4.8 0.8 - - - -
118C ALA* 1.4 79.0 - - - +
120C VAL* 1.3 67.5 + - - +
121C GLN 3.3 3.0 + - - -
131C GLY 5.3 2.1 + - - -
181C THR* 3.7 7.3 - - - +
182C ILE* 3.9 4.3 - - - -
1262C AMP 2.9 37.1 + - - +
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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