Contacts of the strand formed by residues 62 - 68 (chain B) in PDB entry 3A9L
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS 3.2 13.9 - - - -
29B ARG* 3.5 3.1 - - - -
30B GLN* 2.8 23.4 + - - +
31B ASN* 3.0 8.2 + - - +
34B MET 2.9 9.4 + - - -
35B ILE* 3.9 3.6 - - - -
36B TYR 3.0 24.6 + - - +
56B VAL* 3.7 5.1 - - - +
61B GLY* 1.3 75.7 - - - -
63B LEU* 1.3 59.2 + - - +
92B MET* 4.0 4.7 - - - -
96B HIS* 2.6 38.0 + - - -
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 3.5 36.3 - - + +
27B VAL* 3.5 2.5 - - - +
28B LYS* 2.8 48.2 + - + +
35B ILE* 4.2 2.7 - - - -
36B TYR 3.4 4.5 - - - -
52B ILE* 4.1 17.5 - - + -
53B TYR* 3.7 33.4 - - + -
56B VAL* 3.7 23.8 - - + -
61B GLY 3.9 0.2 + - - -
62B SER* 1.3 73.1 - - - +
64B TYR* 1.3 62.3 + - - +
65B LEU* 4.3 6.3 - - + +
92B MET* 3.4 11.4 - - - +
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.4 23.8 - - + +
26B GLU 3.3 5.4 - - - -
27B VAL* 3.9 19.5 - - + -
35B ILE* 3.8 12.8 - - + -
36B TYR 3.2 6.7 + - - -
37B PHE* 3.2 25.0 - + + +
38B SER 3.2 28.5 + - - -
63B LEU* 1.3 75.6 - - - +
65B LEU* 1.3 65.9 + - - +
66B PHE* 3.8 18.9 - - + -
84B PHE* 3.7 16.6 - + - -
86B GLU* 2.5 45.4 + - - +
88B MET* 4.2 2.5 - - + -
89B ALA* 3.2 35.0 - - + -
92B MET* 4.7 2.9 - - + -
93B LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.3 8.3 - - - +
26B GLU* 2.8 48.0 + - + +
38B SER* 3.6 3.1 - - - -
41B ALA* 3.7 15.9 - - + -
49B THR* 3.9 24.5 - - + +
52B ILE* 3.6 34.3 - - + -
53B TYR* 3.5 33.4 - - + -
63B LEU* 4.4 8.3 - - + -
64B TYR* 1.3 86.0 - - - +
66B PHE* 1.3 58.9 + - - +
67B GLN* 3.7 16.6 + - + +
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.9 27.8 - - + -
13B LEU* 4.1 24.7 - - + -
23B TYR* 3.6 42.4 - + + -
24B ASN 3.8 1.8 - - - -
25B ILE* 3.9 18.2 - - + -
38B SER 3.0 8.7 + - - -
39B PRO* 3.4 24.2 - - + +
40B HIS 3.8 0.5 - - - -
41B ALA 2.9 23.9 + - - +
44B ILE* 3.9 11.2 - - + +
64B TYR* 3.8 18.6 - - - +
65B LEU* 1.3 71.6 - - - +
67B GLN* 1.3 60.0 + - - +
77B LEU* 4.2 9.9 - - + -
84B PHE* 3.7 21.1 - + + -
86B GLU* 4.5 0.7 - - + -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 3.2 27.6 - - - +
24B ASN* 2.8 44.5 + - - +
26B GLU* 3.2 24.2 + - - -
41B ALA 3.6 3.1 - - - -
42B GLY* 3.8 13.0 + - - +
44B ILE* 4.4 2.5 - - - -
49B THR* 2.7 33.7 + - - +
53B TYR* 4.2 1.4 + - - -
65B LEU* 3.8 24.9 - - + +
66B PHE* 1.3 76.5 - - - +
68B GLY* 1.3 67.8 + - - +
69B LEU* 4.4 5.7 - - + +
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA 3.8 4.9 - - - -
41B ALA 3.0 13.7 + - - -
42B GLY* 3.6 5.2 - - - -
43B GLY* 3.2 18.4 + - - -
44B ILE* 3.8 17.0 - - - +
67B GLN* 1.3 75.4 - - - +
69B LEU* 1.3 64.1 + - - +
74B ASN* 3.3 19.5 - - - -
77B LEU* 4.0 4.3 - - - -
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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