Contacts of the strand formed by residues 123 - 128 (chain C) in PDB entry 2BG9
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C ASN* 4.2 11.2 - - - +
56C VAL 3.3 7.6 - - - +
57C TRP* 4.7 10.5 - - + +
103C ASN 3.2 2.4 - - - +
104C VAL* 2.5 55.3 - - + +
105C ALA* 3.0 1.4 - - - +
122C PRO* 1.3 93.0 - - + +
124C ALA* 1.3 58.1 + - - +
125C ILE 4.1 0.4 - - - -
149D TRP* 3.2 29.1 - - + +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASN* 2.7 23.1 + - - +
56C VAL* 2.6 48.7 + - + +
58C MET* 5.1 2.5 - - + -
94C LEU* 5.5 2.7 - - + -
102C TYR* 5.2 5.6 - - + -
103C ASN 3.5 3.8 - - - +
105C ALA* 3.4 17.5 - - + -
122C PRO 4.8 0.7 - - - +
123C PRO* 1.3 74.0 - - - +
125C ILE* 1.3 59.1 + - - +
126C PHE* 3.0 13.2 - - + -
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Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 5.9 5.6 - - + -
53C THR* 4.8 14.4 - - + -
54C THR 3.9 3.4 - - - -
55C ASN* 3.3 18.5 - - + +
101C GLN 4.5 2.6 - - - +
102C TYR* 4.4 1.4 - - - -
103C ASN* 3.2 40.6 + - + +
104C VAL* 4.4 18.8 - - + -
123C PRO 4.1 0.2 - - - -
124C ALA* 1.3 67.9 - - - +
126C PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 126 (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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39C LEU* 5.4 2.2 - - + -
53C THR* 2.9 9.9 - - - +
54C THR* 2.6 85.1 + - - -
56C VAL* 3.0 46.9 - - + -
94C LEU* 4.0 25.6 - - + -
97C ASN* 4.9 2.0 - - + -
100C GLY 4.9 7.6 - - - +
101C GLN 5.3 0.2 - - - -
102C TYR* 5.2 3.4 - - - -
124C ALA* 3.0 17.5 - - + -
125C ILE* 1.3 76.5 - - - +
127C ARG* 1.3 69.0 + - - +
128C SER* 4.2 10.8 - - - -
146C LEU* 5.2 9.0 - - + -
148C PHE* 5.3 7.4 - + - -
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Residues in contact with ARG 127 (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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51C THR* 3.5 32.1 - - + +
52C LEU 3.1 4.9 - - - +
53C THR* 4.1 17.2 + - + +
97C ASN 2.4 25.4 - - - +
98C ASN* 4.3 0.9 - - - -
99C ASP 4.3 14.9 + - - +
100C GLY* 4.4 21.5 + - - +
126C PHE* 1.3 75.3 - - - +
128C SER* 1.3 54.9 + - - +
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Residues in contact with SER 128 (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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51C THR* 2.8 10.9 - - - +
52C LEU* 2.6 64.3 + - - +
54C THR* 4.1 6.1 + - - -
97C ASN* 2.6 41.3 - - - +
99C ASP* 5.6 1.8 - - - +
126C PHE* 4.2 5.8 - - - -
127C ARG* 1.3 75.2 - - - +
129C SER* 1.3 59.3 + - - +
130C CYS 3.5 0.7 - - - -
146C LEU* 4.6 5.0 - - - +
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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