Contacts of the strand formed by residues 121 - 127 (chain D) 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 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D ASN* 2.5 28.9 + - - +
55D ARG* 4.0 28.7 - - + +
101D ALA 3.7 6.0 - - - +
102D ILE* 3.6 31.5 - - + +
106D THR* 5.5 6.7 - - + -
119D THR 3.7 6.5 - - - +
120D PRO* 1.3 80.1 - - + +
122D ALA* 1.3 54.5 + - - +
123D ILE* 3.5 3.6 + - - +
148E GLN* 4.7 20.4 - - + +
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D THR 3.9 0.2 - - - +
53D ASN* 2.8 6.7 + - - -
54D VAL* 2.7 45.2 + - - +
56D LEU* 3.8 12.1 - - + -
100D PHE* 3.9 18.2 - - + -
101D ALA 3.5 7.0 - - - -
103D VAL* 3.6 27.8 - - + -
120D PRO 2.5 12.5 + - - +
121D PRO* 1.3 66.7 - - - +
123D ILE* 1.3 58.7 + - - +
124D PHE* 4.4 2.5 + - + -
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLN* 5.8 4.3 - - + +
41D ILE* 4.5 9.6 - - + -
51D GLU* 4.4 13.0 - - - +
52D THR 3.1 9.6 - - - +
53D ASN* 3.1 37.5 - - + +
99D ASP 3.7 0.2 - - - +
101D ALA* 2.7 46.4 + - + +
102D ILE* 4.5 10.8 - - + -
121D PRO 4.1 2.0 - - - +
122D ALA* 1.3 72.7 - - - +
124D PHE* 1.3 64.6 + - - +
95E VAL 5.2 2.7 - - - +
96E ASP* 3.6 41.7 - - - +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D VAL 3.2 2.6 - - - +
51D GLU* 3.0 26.5 - - - -
52D THR* 3.0 19.7 + - + +
54D VAL* 4.9 15.9 - - + -
92D LEU* 3.0 49.6 - - + -
96D ALA* 4.3 3.6 - - - -
98D GLY 3.5 9.6 - - - -
99D ASP 2.8 27.1 - - - +
100D PHE* 3.3 38.1 - + - -
122D ALA* 5.2 4.3 - - + -
123D ILE* 1.3 75.9 - - - +
125D LYS* 1.3 85.1 + - - +
126D SER* 4.2 9.9 - - - -
146D LEU* 5.7 1.8 - - + -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D ILE* 2.7 53.5 - - + +
50D VAL 3.4 0.4 - - - -
51D GLU* 3.4 32.3 + - + +
97D ASP* 3.2 24.1 + - - +
98D GLY* 2.6 40.7 + - - -
99D ASP 4.4 0.2 + - - -
124D PHE* 1.3 83.7 - - - +
126D SER* 1.3 60.0 + - - +
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 3.2 12.1 - - - +
50D VAL* 2.6 55.2 + - - +
52D THR* 5.9 2.2 - - - -
95D ASN* 3.3 20.9 + - - -
96D ALA 4.3 0.7 - - - +
97D ASP* 3.7 8.1 - - - +
124D PHE* 4.2 13.9 - - - -
125D LYS* 1.3 73.7 - - - +
127D TYR* 1.3 64.4 + - - +
128D CYS* 4.1 1.0 + - - -
144D MET* 4.5 9.5 - - - -
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 4.5 17.8 + - - -
43C ILE* 4.3 25.3 - - + +
185C THR* 5.5 6.2 + - - +
187C ASN* 4.8 9.7 + - - +
47D ASN 4.1 4.3 - - - -
48D GLN* 2.8 38.8 + - + -
49D ILE* 3.9 15.5 - - + -
94D ASN 2.3 43.6 - - - +
95D ASN* 2.6 24.1 + - - +
97D ASP* 3.7 19.1 - - + -
126D SER* 1.3 80.5 + - - +
128D CYS* 1.3 54.1 + - - +
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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