Contacts of the helix formed by residues 87 - 98 (chain A) in PDB entry 3BGD
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 SER 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS* 4.3 16.7 + - - +
28A TRP* 3.3 34.9 - - - +
85A GLU* 2.9 24.1 + - - +
86A ILE* 1.3 76.7 - - - +
88A GLU* 1.3 61.9 + - - +
89A ILE* 3.4 7.3 + - - +
90A GLY 3.2 16.0 + - - -
91A ILE* 3.1 18.0 + - - +
127A CYS* 4.0 2.7 - - - -
300A SAH 4.3 1.1 - - - -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE 3.7 1.0 + - - -
87A SER* 1.3 72.1 + - - +
89A ILE* 1.3 59.0 + - + +
91A ILE* 3.2 4.2 + - - +
92A ARG* 2.2 76.2 + - - +
104A GLU* 4.9 0.2 - - - +
114A LYS* 3.0 30.2 + - - -
116A PHE* 3.5 12.1 - - + -
127A CYS* 3.6 18.4 - - - -
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 4.2 8.3 - - + +
29A VAL* 3.6 42.4 - - + +
31A ARG* 3.9 25.1 - - - +
87A SER* 3.2 8.7 + - - +
88A GLU* 1.3 80.0 - - + +
90A GLY* 1.3 57.4 + - - +
92A ARG* 3.5 5.0 + - - +
93A GLU* 3.0 31.5 + - - +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 3.6 36.1 - - - -
66A GLY 4.0 7.6 - - - +
67A LYS* 3.6 11.8 - - - +
85A GLU* 4.9 1.3 - - - -
87A SER* 3.2 11.4 + - - -
89A ILE* 1.3 76.9 - - - +
91A ILE* 1.3 65.6 + - - +
93A GLU* 3.4 1.3 + - - +
94A PHE* 3.1 18.5 + - - +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY 4.7 2.0 - - - +
85A GLU* 3.6 29.6 - - + +
87A SER 3.1 8.1 + - - +
88A GLU* 3.2 7.2 + - - +
90A GLY* 1.3 76.6 - - - +
92A ARG* 1.3 62.4 + - - +
94A PHE* 3.3 12.6 + - - +
95A PHE* 3.3 22.9 + - + -
116A PHE* 3.4 38.4 - - + -
125A LEU* 4.0 23.8 - - + +
126A TYR 3.9 7.9 - - - +
127A CYS* 3.6 40.8 - - + +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU* 2.2 69.5 + - - +
89A ILE* 4.2 5.2 - - - +
91A ILE* 1.3 74.1 - - - +
93A GLU* 1.3 61.4 + - - +
95A PHE* 3.4 4.3 + - - +
96A ALA* 3.0 27.8 + - - +
102A TYR* 3.3 36.1 + - + +
104A GLU* 2.4 30.3 + - - +
116A PHE* 2.9 22.3 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TRP* 4.0 3.3 - - - -
31A ARG* 2.5 43.7 + - - -
67A LYS* 2.3 40.9 + - + -
89A ILE* 3.0 22.6 + - - +
90A GLY* 3.7 5.8 - - - +
92A ARG* 1.3 76.4 - - - +
94A PHE* 1.3 59.1 + - - +
96A ALA* 4.0 6.0 - - + +
97A GLU* 2.8 45.2 + - + +
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY 4.6 0.7 - - - +
67A LYS* 3.5 38.8 - - + +
68A ALA 3.3 20.4 - - - -
71A MET* 3.8 23.1 - - + -
72A LYS* 4.2 6.7 - - + -
90A GLY 3.1 8.1 + - - +
91A ILE 3.3 9.4 + - - +
93A GLU* 1.3 77.1 - - - +
95A PHE* 1.3 67.5 + + - +
97A GLU* 3.7 2.4 - - - -
98A GLN* 2.7 72.7 + - + +
100A LEU* 4.6 0.4 - - + -
123A ILE* 3.9 40.2 - - + -
125A LEU* 3.9 18.6 - - + -
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.3 20.4 + - + -
92A ARG 3.4 3.5 + - - +
93A GLU 3.3 0.2 - - - -
94A PHE* 1.3 91.7 - + - +
96A ALA* 1.3 61.6 + - - +
98A GLN* 4.5 1.3 - - - +
99A ASN* 3.0 18.2 + - - -
100A LEU* 3.1 34.3 + - + +
102A TYR* 3.4 52.9 - + + -
116A PHE* 3.7 38.1 - - + -
118A SER* 3.9 24.7 - - - -
123A ILE* 4.3 6.1 - - + -
125A LEU* 3.7 25.1 - - + -
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Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ARG 3.0 18.1 + - - +
93A GLU* 4.0 8.1 - - + +
95A PHE* 1.3 75.1 - - - +
97A GLU* 1.3 64.6 + - + +
99A ASN* 3.3 13.2 + - - +
102A TYR* 5.3 1.4 - - - -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A HIS* 3.9 11.3 + - - -
67A LYS* 2.7 47.1 + - - +
69A ILE* 4.8 2.1 - - - +
93A GLU* 2.8 25.2 + - + +
94A PHE* 3.7 3.8 - - - +
96A ALA* 1.3 79.2 - - + +
98A GLN* 1.3 75.4 + - - +
99A ASN* 3.2 3.3 + - - +
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS 4.8 0.2 + - - -
69A ILE* 3.3 37.4 - - - +
72A LYS* 3.6 34.8 + - + +
94A PHE* 2.7 58.8 + - + +
95A PHE 4.4 1.1 - - - +
97A GLU* 1.3 83.3 + - - +
99A ASN* 1.3 70.8 + - - +
100A LEU* 3.4 16.0 + - + +
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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