Contacts of the strand formed by residues 36 - 43 (chain B) in PDB entry 3SAJ
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 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ASN 3.1 13.1 + - - +
6B ASN* 3.4 12.6 - - - +
7B ILE 2.7 33.1 + - - -
28B LEU 5.7 4.3 - - - -
31B LEU* 5.0 17.5 - - + +
32B THR 6.0 1.6 - - - +
33B GLU 4.4 7.0 - - - +
34B PRO* 3.7 4.3 - - + +
35B PRO* 1.3 71.6 - - - +
37B LEU* 1.3 67.3 + - - +
38B LEU* 3.5 11.6 + - + +
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Residues in contact with LEU 37 (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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7B ILE* 3.4 30.5 - - + -
9B ILE* 3.8 17.3 - - + -
28B LEU* 3.8 26.9 - - + +
31B LEU* 4.0 21.3 - - + +
35B PRO 3.7 6.3 + - - +
36B LYS* 1.3 83.0 + - - +
38B LEU* 1.3 59.3 + - - +
39B PRO* 3.5 9.8 - - - +
279B VAL 4.0 11.2 - - - +
282B MET* 4.0 29.8 - - + +
283B ALA* 4.0 10.3 - - + +
286B PHE* 4.2 14.4 - - + -
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Residues in contact with LEU 38 (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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6B ASN* 4.7 24.7 - - + +
7B ILE 2.7 16.5 + - - +
8B GLN* 3.4 13.1 - - + +
9B ILE* 2.8 27.3 + - - -
36B LYS* 3.5 12.3 + - + +
37B LEU* 1.3 71.8 - - - +
39B PRO* 1.3 82.7 - - + +
40B GLN* 3.8 19.0 + - + +
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Residues in contact with PRO 39 (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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9B ILE* 3.5 9.2 - - + +
24B PHE* 3.9 27.1 - - + -
28B LEU* 3.7 20.9 - - + -
37B LEU* 3.5 9.6 - - - +
38B LEU* 1.3 96.4 - - + +
40B GLN* 1.3 66.1 + - - +
41B ILE* 3.9 6.5 - - + -
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Residues in contact with GLN 40 (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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8B GLN* 4.4 19.3 - - - +
9B ILE 2.8 14.0 + - - +
10B GLY* 3.9 3.3 - - - -
11B GLY 3.5 11.3 + - - -
38B LEU* 4.2 14.9 - - + +
39B PRO* 1.3 78.8 - - - +
41B ILE* 1.3 66.8 + - - +
42B ASP* 3.9 2.9 + - - +
59B GLN* 4.0 7.4 + - + +
62B LYS* 2.5 61.2 - - + +
64B VAL* 4.0 9.4 - - + +
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Residues in contact with ILE 41 (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 GLY 4.5 0.9 - - - -
11B GLY* 3.4 28.3 - - - +
13B PHE* 3.8 25.6 - - + -
21B HIS* 3.7 33.9 - - + +
24B PHE* 3.9 30.5 - - + -
39B PRO* 3.9 3.2 - - + -
40B GLN* 1.3 84.0 - - - +
42B ASP* 1.3 71.9 + - - +
43B ILE* 6.0 2.9 - - + -
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Residues in contact with ASP 42 (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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11B GLY 2.8 12.1 + - - +
12B LEU* 3.8 1.8 - - + -
13B PHE* 3.0 28.3 + - - +
40B GLN* 4.6 2.7 - - - +
41B ILE* 1.3 84.1 - - - +
43B ILE* 1.3 64.2 + - - +
44B VAL* 3.5 0.9 + - - +
55B ARG* 3.2 52.2 + - + +
58B SER* 5.5 1.0 + - - -
59B GLN* 2.8 31.8 + - - +
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Residues in contact with ILE 43 (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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13B PHE* 3.3 6.7 - - + +
14B PRO 3.7 20.6 - - - +
15B ASN 3.8 18.2 - - - +
16B GLN* 3.3 42.6 - - + +
41B ILE* 6.0 3.4 - - + -
42B ASP* 1.3 73.9 - - - +
44B VAL* 1.3 62.9 + - - +
51B GLU* 5.3 0.3 - - - +
55B ARG* 4.4 13.5 + - - +
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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