Contacts of the strand formed by residues 42 - 50 (chain B) in PDB entry 1SN8
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 TYR 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 4.0 9.2 - - - -
39B ALA 3.6 15.8 + - - -
40B ASN* 3.5 23.2 + - - -
41B ILE* 1.3 90.9 - - - +
43B LYS* 1.3 59.8 + - - +
44B GLY 3.9 0.2 - - - -
60B TYR* 3.7 50.2 - + + +
100B VAL 3.6 0.3 - - - +
101B ILE* 3.4 8.8 - - - +
102B VAL* 2.8 40.7 + - + +
103B GLN* 4.6 3.1 - - - -
104B ILE* 3.9 26.4 - - + +
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Residues in contact with LYS 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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40A ASN* 4.6 21.6 + - - +
41A ILE* 3.9 17.4 - - + +
103A GLN* 4.2 7.1 + - - -
120A ILE* 4.3 12.1 - - - -
121A SER* 2.7 35.8 + - - +
122A LEU* 3.9 17.9 - - + -
42B TYR* 1.3 74.6 - - - +
44B GLY* 1.3 60.1 + - - +
59B ASP 4.2 1.2 - - - +
60B TYR* 3.8 14.4 - - - +
99B GLU* 3.4 32.2 + - + +
100B VAL 3.5 3.1 - - - -
101B ILE* 4.8 0.4 - - - +
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Residues in contact with GLY 44 (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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42B TYR 3.9 1.4 - - - -
43B LYS* 1.3 75.2 - - - +
45B LYS* 1.3 62.0 + - - -
58B VAL* 3.5 18.6 - - - -
59B ASP 3.4 9.2 - - - -
60B TYR* 4.0 5.6 - - - -
98B GLN 3.7 0.3 - - - +
99B GLU* 3.0 9.2 - - - +
100B VAL* 2.8 37.3 + - - +
102B VAL* 4.6 1.9 - - - +
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Residues in contact with LYS 45 (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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123A ALA* 4.5 11.1 - - - +
44B GLY* 1.3 73.6 - - - -
46B ILE* 1.3 68.6 + - - +
47B THR* 3.3 4.8 + - + +
58B VAL* 3.4 3.3 - - - -
59B ASP* 2.9 40.1 + - + +
97B GLY* 3.3 40.0 + - - +
98B GLN 3.4 3.4 - - - +
99B GLU* 4.4 16.7 - - + +
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Residues in contact with ILE 46 (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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45B LYS* 1.3 73.1 - - - +
47B THR* 1.3 60.3 + - - +
48B ARG 4.1 3.4 - - - +
49B ILE* 3.8 29.4 - - + -
56B ALA* 4.0 5.8 - - + -
57B PHE 3.5 8.3 - - - +
58B VAL* 3.9 23.3 - - + -
68B LEU* 4.4 0.9 - - + -
94B LEU* 3.7 26.5 - - + -
95B ARG 3.4 24.5 - - - +
96B GLU* 3.4 3.3 - - - +
97B GLY* 2.9 25.8 + - - -
98B GLN* 2.9 27.3 + - + +
100B VAL* 4.1 19.5 - - + -
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Residues in contact with THR 47 (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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45B LYS* 3.8 8.5 - - + +
46B ILE* 1.3 74.0 - - - +
48B ARG* 1.3 65.4 + - - +
57B PHE* 2.9 17.0 + - - +
59B ASP* 3.7 23.3 - - + +
65B HIS* 3.0 39.9 + - + -
96B GLU* 3.1 28.8 - - - +
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Residues in contact with ARG 48 (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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46B ILE* 3.7 1.4 - - - +
47B THR* 1.3 88.8 + - - +
49B ILE* 1.3 75.3 - - - +
50B GLU* 4.3 19.7 + - - +
53B LEU* 5.7 0.8 - - - +
56B ALA* 3.3 5.5 - - - +
57B PHE* 2.8 77.1 + - + +
65B HIS* 6.2 0.2 + - - -
96B GLU* 4.5 6.3 - - - +
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Residues in contact with ILE 49 (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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46B ILE* 3.8 11.4 - - + -
48B ARG* 1.3 85.8 - - - +
50B GLU* 1.3 65.7 + - - +
51B PRO* 3.3 13.7 - - + +
55B ALA 3.8 2.0 - - - -
56B ALA* 4.3 5.6 - - + -
90B ILE* 3.7 30.3 - - + -
91B LYS* 4.2 14.6 - - + -
94B LEU* 3.2 38.8 - - + +
95B ARG* 3.6 16.6 - - - +
96B GLU* 4.0 7.6 + - + +
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Residues in contact with GLU 50 (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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48B ARG* 4.2 18.5 + - - +
49B ILE* 1.3 75.3 - - - +
51B PRO* 1.3 73.1 - - - +
52B SER* 3.1 39.6 + - - +
53B LEU* 3.1 28.2 + - + -
54B GLU 3.1 16.3 + - - -
55B ALA 2.8 21.7 + - - +
57B PHE* 4.4 12.1 - - + -
90B ILE* 4.3 1.8 - - - -
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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