Contacts of the strand formed by residues 38 - 43 (chain L) in PDB entry 5GAG
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 38 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24L VAL* 4.6 1.4 - - - +
25L LEU* 3.6 41.9 + - + +
36L GLY 4.7 1.8 - - - +
37L ASP* 1.3 77.7 + - - +
39L ILE* 1.3 72.4 + - - +
59L LYS* 4.5 4.3 - - + -
60L ALA 3.2 8.3 - - - +
61L VAL* 4.7 1.1 - - + -
87L LEU* 3.6 24.9 - - + -
92L GLU* 3.8 22.7 - - - +
111L LYS* 3.9 11.7 - - - +
112L PHE* 3.4 31.6 - - + -
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Residues in contact with ILE 39 (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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2L ILE* 4.9 3.6 - - + -
8L LEU* 4.5 13.2 - - + -
21L CYS* 3.9 21.1 - - + -
23L LYS 3.4 9.0 - - - +
24L VAL* 3.6 25.1 - - + -
25L LEU* 3.8 11.2 - - - +
33L ALA* 3.8 15.0 - - + -
38L ILE* 1.3 80.1 - - - +
40L LYS* 1.3 59.7 + - - +
41L ILE* 3.6 24.7 - - + -
59L LYS* 3.3 7.8 - - - +
60L ALA* 2.9 42.8 + - + +
62L VAL* 4.1 19.1 - - + -
84L CYS* 5.5 0.2 - - - -
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Residues in contact with LYS 40 (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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2561A U 3.5 13.5 - - - +
2562A U 2.6 29.0 + - - +
21L CYS* 3.7 1.2 - - - -
22L ILE* 2.9 37.7 + - + -
23L LYS* 3.2 29.0 + - + +
25L LEU* 4.1 10.9 - - + +
39L ILE* 1.3 72.4 - - - +
41L ILE* 1.3 67.8 + - - +
57L VAL* 4.2 20.0 - - + -
58L LEU 3.6 6.5 - - - +
59L LYS* 3.5 24.9 - - + +
89L ASN* 2.9 30.9 + - - +
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Residues in contact with ILE 41 (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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19L VAL* 3.6 29.8 - - + -
20L MET 3.4 13.0 - - - +
21L CYS* 4.4 2.2 - - - -
22L ILE* 4.1 6.5 - - - +
39L ILE* 3.6 29.8 - - + -
40L LYS* 1.3 81.4 - - - +
42L THR* 1.3 65.4 + - - +
57L VAL* 3.5 7.7 - - - +
58L LEU* 2.8 51.0 + - + +
60L ALA* 3.9 12.8 - - + -
86L LEU* 3.5 32.1 - - + -
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Residues in contact with THR 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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1952A A 3.4 44.1 + - + +
19L VAL* 3.3 6.4 - - - +
20L MET* 3.0 40.2 + - + +
22L ILE* 3.8 21.0 - - + +
41L ILE* 1.3 75.5 - - - +
43L ILE* 1.3 73.9 + - - +
44L LYS* 4.0 15.3 - - - -
55L GLY 3.7 15.0 + - - -
56L ASP 3.5 6.3 - - - -
57L VAL* 5.0 1.8 - - - -
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Residues in contact with ILE 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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1952A A 4.4 0.7 + - - -
16L ALA* 4.6 6.1 - - + -
19L VAL* 4.3 16.2 - - + -
42L THR* 1.3 82.8 + - - +
44L LYS* 1.3 61.9 + - - +
45L GLU 3.1 29.8 - - - +
46L ALA* 5.1 1.3 - - + -
52L VAL* 3.7 39.3 - - + -
53L LYS 3.9 19.1 - - - +
54L LYS* 3.8 3.7 - - - +
55L GLY* 2.8 28.6 + - - +
56L ASP* 3.2 17.3 + - + +
58L LEU* 4.3 14.1 - - + -
86L LEU* 4.4 9.4 - - + -
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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