Contacts of the strand formed by residues 102 - 107 (chain D) in PDB entry 2BP1
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 LYS 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D THR* 2.9 29.9 + - + +
71D GLU* 3.6 20.6 - - + +
72D LEU* 2.8 30.7 + - - +
99D CYS* 3.0 28.1 + - - +
100D ARG* 4.2 7.8 + - - +
101D VAL* 1.3 81.0 + - - +
103D ILE* 1.3 61.0 + - - +
137D ASP* 3.2 29.8 + - + +
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Residues in contact with ILE 103 (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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71D GLU* 5.8 1.6 - - - -
72D LEU* 3.8 26.2 - - + +
74D THR* 4.0 13.7 - - + -
87D LEU* 4.3 10.3 - - + -
94D LEU* 3.9 42.2 - - + -
95D GLY 5.1 1.1 - - - +
102D LYS* 1.3 75.2 - - - +
104D ALA* 1.3 74.2 + - - +
131D LEU* 4.1 15.9 - - + -
133D CYS* 4.7 2.5 - - - -
135D GLN 4.6 3.1 - - - +
136D VAL* 3.9 24.1 - - + +
137D ASP* 2.7 37.0 + - - +
138D LEU* 3.2 6.7 + - - +
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Residues in contact with ALA 104 (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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42D VAL* 6.4 0.2 - - + -
71D GLU* 5.3 4.9 - - + +
72D LEU 2.8 15.1 + - - +
73D ASP* 4.0 8.1 - - + +
74D THR* 2.9 33.1 + - - +
103D ILE* 1.3 75.6 - - - +
105D THR* 1.3 60.3 + - - +
138D LEU* 3.2 22.0 - - + +
140D TYR* 3.7 27.6 - - + +
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Residues in contact with THR 105 (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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74D THR* 3.5 13.5 - - - -
75D ALA* 3.4 9.4 - - - -
76D PHE 3.4 2.3 + - - -
84D GLU* 2.7 23.7 + - - -
104D ALA* 1.3 75.3 - - - +
106D LYS* 1.3 69.9 + - - +
124D LEU* 4.2 12.1 - - + -
127D SER* 3.7 19.3 + - - +
131D LEU* 4.4 3.4 - - + -
136D VAL* 3.9 25.8 - - + +
138D LEU 3.1 4.0 + - - -
139D PHE* 3.5 9.9 - - + -
140D TYR* 2.8 28.2 + - - -
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ASP* 2.7 27.3 + - - -
74D THR 3.0 21.4 + - - +
75D ALA* 3.9 4.2 - - + +
76D PHE* 3.1 28.4 + - - +
78D TYR* 3.1 18.6 + - - -
105D THR* 1.3 88.2 + - - +
107D ALA* 1.3 59.2 + - - +
108D ASN 4.3 0.2 + - - -
127D SER* 4.9 0.7 + - - -
139D PHE* 4.4 3.8 - - - -
140D TYR* 3.2 25.4 - - + +
142D HIS* 3.6 43.7 + - + +
172D SER* 5.1 0.7 - - - -
198D GLN* 3.0 34.1 - - - +
1361D NDP 3.9 5.6 - - - +
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Residues in contact with ALA 107 (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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106D LYS* 1.3 72.4 - - - +
108D ASN* 1.3 60.8 + - - +
115D LEU* 3.9 16.5 - - + +
120D VAL* 4.7 7.0 - - + -
123D GLN* 3.1 26.7 - - + +
139D PHE* 3.6 27.4 - - + -
140D TYR 2.9 8.0 + - - +
141D LEU* 3.9 4.2 - - + -
142D HIS* 2.9 24.2 + - - -
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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