Contacts of the strand formed by residues 98 - 101 (chain C) in PDB entry 3OEH
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 98 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 4.7 11.6 - - - +
95C ASN* 5.2 10.0 - - - +
96C ILE 3.8 8.6 - - - +
97C VAL* 1.3 81.6 - - - +
99C VAL* 1.3 71.4 + - - +
113C LEU* 4.3 15.8 - - - +
128C ARG* 2.8 44.6 + - + +
129C SER 3.3 15.7 - - - +
130C ARG* 3.7 10.5 - - + +
131C ALA 3.8 2.7 - - - +
251C THR* 4.6 1.9 - - - +
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 1.3 81.5 - - - +
100C PRO* 1.4 75.1 - - + +
101C VAL* 3.7 3.0 - - + +
112C ALA 3.7 0.9 - - - +
113C LEU 3.4 29.2 - - - +
114C GLY* 3.8 4.5 - - - +
128C ARG* 3.1 9.8 - - - +
129C SER 2.8 36.2 + - - +
130C ARG 4.7 1.3 - - - +
251C THR* 3.6 47.8 - - + +
254C SER* 3.9 11.9 - - - +
255C ILE* 4.7 6.1 - - + -
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Residues in contact with PRO 100 (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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99C VAL* 1.4 89.8 - - + +
101C VAL* 1.3 62.2 + - - +
105C LEU* 3.8 12.6 - - + +
113C LEU 3.8 13.2 - - - +
114C GLY* 4.1 22.2 - - - +
123C ILE* 4.9 10.3 - - + -
125C ALA* 3.7 18.8 - - + -
127C GLY 3.4 8.5 - - - +
128C ARG* 3.4 24.4 - - - +
255C ILE* 3.7 14.4 - - - +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 3.7 11.4 - - + +
100C PRO* 1.3 80.6 - - - +
102C GLY* 1.3 59.7 + - - +
105C LEU* 3.6 8.7 - - - -
125C ALA* 3.5 2.3 - - - -
126C ALA 2.8 23.9 + - - -
127C GLY* 2.8 32.1 + - - +
128C ARG 4.1 0.2 - - - +
129C SER* 3.8 23.1 - - - +
254C SER 3.7 23.6 - - - +
255C ILE* 3.9 12.6 - - + +
258C TRP* 3.8 25.6 - - + -
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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
------------------------------------------------------------
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