Contacts of the strand formed by residues 42 - 48 (chain d) in PDB entry 5GJQ
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 42 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36d PHE 3.9 0.7 - - - +
38d MET* 3.2 41.9 + - + -
39d SER* 3.7 29.3 + - - +
40d GLU 3.7 1.6 - - - -
41d LYS* 1.4 87.1 - - + +
43d LEU* 1.3 68.8 + - - +
64d VAL* 5.4 1.1 - - + -
75d LEU* 3.6 27.4 - - + +
77d PRO* 3.9 27.4 - - + -
80d ALA* 4.0 12.3 - - + -
104d LEU* 3.6 18.4 - - + -
105d ALA 3.4 9.6 - - - +
183d ILE* 4.4 0.2 - - - -
188d ILE* 3.9 7.3 - - - +
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Residues in contact with LEU 43 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15d VAL* 3.8 26.0 - - + -
35d MET* 4.0 7.6 - - + -
36d PHE 3.5 28.5 - - - +
37d LYS* 4.0 13.7 - - - +
42d ILE* 1.3 75.4 - - - +
44d LEU* 1.3 59.0 - - - +
45d LEU* 4.1 12.0 - - + +
103d LEU 3.8 0.5 - - - +
104d LEU* 3.4 7.8 - - - +
105d ALA* 2.8 34.8 + - + +
181d ARG* 3.8 22.7 - - + -
183d ILE* 3.7 17.7 - - + +
188d ILE* 3.7 33.2 - - + -
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Residues in contact with LEU 44 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35d MET* 3.5 0.2 - - - -
36d PHE* 2.9 50.6 + - + +
38d MET* 3.7 32.3 - - + -
42d ILE 4.3 0.2 - - - -
43d LEU* 1.3 72.7 - - - +
45d LEU* 1.3 64.0 + - - +
46d CYS* 3.7 5.8 + - + -
56d PHE* 5.3 2.7 - - + -
57d ALA* 4.2 24.5 - - + +
60d ILE* 4.3 12.3 - - + -
84d THR* 5.4 0.9 - - + -
102d LEU* 3.7 30.1 - - + -
103d LEU 3.5 15.5 - - - +
104d LEU* 4.0 20.9 - - + -
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Residues in contact with LEU 45 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4d LEU* 3.5 35.9 - - + +
15d VAL* 4.1 24.7 - - + -
16d ALA 4.3 6.5 - - - +
17d SER* 3.9 9.2 - - - -
34d LYS 3.6 4.5 - - - -
35d MET* 3.4 40.8 - - + +
43d LEU* 4.1 16.4 - - + +
44d LEU* 1.3 74.8 - - - +
46d CYS* 1.3 59.4 + - - +
102d LEU* 3.1 8.5 - - - +
103d LEU* 2.8 51.5 + - + +
105d ALA* 5.3 0.9 - - + -
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Residues in contact with CYS 46 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2d GLU* 5.0 0.2 - - - +
34d LYS* 3.2 23.3 + - - +
36d PHE* 4.7 6.1 - - + -
44d LEU* 3.7 6.2 + - + +
45d LEU* 1.3 75.3 - - - +
47d VAL* 1.3 73.2 + - - +
53d THR* 3.7 29.2 - - - +
56d PHE* 4.6 10.1 - - - -
57d ALA* 4.5 13.5 - - + -
100d VAL* 3.6 33.9 - - - -
101d ASN 3.8 3.8 - - - -
102d LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 47 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1d MET* 5.5 3.1 - - - -
2d GLU* 3.4 44.9 - - + +
4d LEU* 3.7 33.2 - - + -
34d LYS* 3.8 9.9 - - + -
46d CYS* 1.3 84.6 - - - +
48d GLY* 1.3 63.8 + - - +
53d THR* 3.3 8.5 - - - -
100d VAL* 3.4 5.4 - - - -
101d ASN* 2.8 47.9 + - + +
132d HIS* 4.9 7.4 - - + -
133d GLY* 5.4 2.5 - - - +
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Residues in contact with GLY 48 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2d GLU* 3.1 26.5 + - - +
47d VAL* 1.3 78.0 - - - +
49d GLU* 1.3 66.3 + - - +
50d ALA 3.8 0.3 + - - -
53d THR* 3.3 4.2 - - - +
99d HIS* 3.7 6.5 - - - -
100d VAL* 4.8 0.2 - - - -
101d ASN* 4.9 3.8 - - - -
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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