Contacts of the strand formed by residues 41 - 47 (chain L) in PDB entry 3SDI
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 ILE 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L ASP* 3.8 3.4 + - - +
37L CYS* 2.8 29.6 + - + +
38L GLY 3.4 12.0 + - - +
39L ASP* 3.2 8.9 - - + +
40L ASN* 1.3 84.8 - - - +
42L VAL* 1.3 74.8 + - - +
43L MET* 5.3 0.2 - - + -
59L PHE* 4.3 24.5 - - + -
63L VAL* 5.3 1.1 - - + -
74L LEU* 3.6 28.3 - - + +
75L SER 4.6 2.2 - - - +
76L ILE* 4.0 27.6 - - + +
79L ALA* 3.8 22.4 - - + -
101L ILE* 4.4 9.4 - - + -
102L ALA 3.6 3.6 - - - -
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Residues in contact with VAL 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LEU* 3.6 31.4 - - + +
34L VAL* 4.7 0.2 - - + -
35L PHE 3.2 7.9 - - - +
36L ASP* 4.3 3.4 - - - -
41L ILE* 1.3 78.6 - - - +
43L MET* 1.3 62.1 + - - +
101L ILE* 3.2 8.7 - - - +
102L ALA* 3.0 48.0 + - + +
176L LEU* 3.7 30.5 - - + -
178L VAL* 3.7 24.5 - - + -
184L VAL* 4.1 13.0 - - + -
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Residues in contact with MET 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14L LEU* 3.8 4.2 - - - +
33L LYS 3.8 0.9 - - - +
34L VAL* 3.4 1.0 - - - -
35L PHE* 2.8 40.0 + - - -
37L CYS* 3.5 17.3 - - - -
41L ILE* 5.3 0.2 - - + -
42L VAL* 1.3 77.0 - - - +
44L SER* 1.3 67.3 + - - +
45L ALA* 5.1 1.1 - - + -
55L LEU* 4.1 28.0 - - + -
56L VAL* 4.1 21.1 - - + -
59L PHE* 3.7 32.3 - - + -
83L ILE* 3.7 26.5 - - + -
99L THR* 4.0 16.2 - - - +
100L ILE 3.5 5.4 - - - +
101L ILE* 3.5 14.8 - - + -
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Residues in contact with SER 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L ILE* 3.2 38.0 - - - +
14L LEU* 3.7 13.9 - - - +
33L LYS* 2.5 26.3 + - - +
34L VAL* 4.1 4.5 - - - -
43L MET* 1.3 76.3 - - - +
45L ALA* 1.3 61.4 + - - +
46L ASN 4.1 0.7 - - - -
56L VAL* 5.1 1.6 - - - -
98L HIS 4.0 0.3 - - - +
99L THR* 3.3 4.7 + - - -
100L ILE 2.9 34.5 + - - +
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Residues in contact with ALA 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L LYS* 4.2 7.4 + - - +
43L MET* 5.1 0.9 - - + -
44L SER* 1.3 76.8 + - - +
46L ASN* 1.3 61.7 + - - +
47L GLY 4.1 0.7 + - - -
48L PHE 5.2 0.2 - - - +
49L ALA* 5.5 2.3 - - - -
52L GLY* 3.6 34.7 - - - +
55L LEU* 4.3 9.0 - - + -
56L VAL* 4.5 9.3 - - + +
97L VAL* 3.6 22.7 - - + +
98L HIS 3.6 5.4 - - - -
99L THR* 3.9 10.5 - - - -
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Residues in contact with ASN 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1L GLY 3.1 18.6 + - - +
1L GLY 3.0 12.3 - - - +
2L THR* 4.3 0.9 - - - -
3L ILE* 3.9 28.9 - - + -
33L LYS* 2.9 37.1 - - - +
44L SER* 4.1 0.4 - - - -
45L ALA* 1.3 73.1 - - - +
47L GLY* 1.3 61.1 + - - +
97L VAL* 3.3 3.1 - - - -
98L HIS* 2.9 37.7 + - - +
128L GLY* 3.0 32.1 - - - +
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Residues in contact with GLY 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-4L GLY 4.7 1.1 - - - -
-3L ASP* 4.6 8.5 - - - -
-2L ASN* 3.1 28.7 + - - +
-1L GLY 4.1 4.2 + - - +
45L ALA 4.1 1.2 + - - -
46L ASN* 1.3 84.8 - - - +
48L PHE* 1.3 62.2 + - - -
49L ALA* 3.3 3.8 + - - +
96L TYR 3.8 5.8 - - - -
97L VAL* 4.3 0.2 - - - +
98L HIS* 6.3 0.2 - - - -
128L GLY* 6.1 1.1 - - - -
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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