Contacts of the strand formed by residues 42 - 48 (chain r) 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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36r PHE 3.9 1.0 - - - +
37r LYS* 3.9 2.6 - - - -
38r MET* 3.2 45.1 + - + -
39r SER* 3.7 31.5 + - - +
40r GLU 3.7 1.2 - - - -
41r LYS* 1.3 87.5 - - + +
43r LEU* 1.3 68.0 + - - +
64r VAL* 5.5 1.8 - - + -
75r LEU* 3.9 20.6 - - + +
76r SER 4.2 0.2 - - - +
77r PRO* 3.8 29.2 - - + -
80r ALA* 4.0 12.6 - - + -
104r LEU* 3.8 19.7 - - + -
105r ALA 3.5 9.9 - - - +
188r ILE* 4.1 2.4 - - - +
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Residues in contact with LEU 43 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15r VAL* 3.8 24.7 - - + -
35r MET* 4.0 9.6 - - + -
36r PHE 3.4 28.9 - - - +
37r LYS* 4.0 10.5 - - + +
42r ILE* 1.3 74.0 - - - +
44r LEU* 1.3 60.4 + - - +
45r LEU* 4.1 10.7 - - + +
103r LEU 3.9 0.9 - - - +
104r LEU* 3.6 6.8 - - - +
105r ALA* 2.9 35.8 + - + +
181r ARG* 3.9 22.7 - - + -
183r ILE* 3.6 29.5 - - + +
188r ILE* 3.8 24.2 - - + -
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Residues in contact with LEU 44 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34r LYS 3.7 0.2 - - - +
36r PHE* 3.0 53.2 + - + +
38r MET* 3.8 31.4 - - + -
43r LEU* 1.3 72.6 - - - +
45r LEU* 1.3 62.0 + - - +
46r CYS* 5.1 4.0 - - + -
56r PHE* 5.2 1.8 - - + -
57r ALA* 4.4 18.6 - - + +
60r ILE* 4.2 17.9 - - + -
84r THR* 5.2 1.1 - - + -
102r LEU* 3.7 30.5 - - + -
103r LEU 3.6 12.6 - - - +
104r LEU* 4.1 19.5 - - + -
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Residues in contact with LEU 45 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4r LEU* 3.5 37.5 - - + +
5r ILE 5.8 0.4 - - - +
15r VAL* 4.1 18.6 - - + -
16r ALA 4.5 5.8 - - - +
17r SER* 3.8 10.3 - - - -
34r LYS 3.7 3.4 - - - +
35r MET* 3.6 41.5 - - + -
43r LEU* 4.1 21.1 - - + +
44r LEU* 1.3 76.1 - - - +
46r CYS* 1.3 59.5 + - - +
102r LEU* 3.2 7.6 - - - +
103r LEU* 2.9 46.0 + - + +
105r ALA* 5.8 0.4 - - + -
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Residues in contact with CYS 46 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2r GLU* 4.9 0.9 - - - +
4r LEU* 4.2 0.2 - - - +
34r LYS* 3.3 23.2 + - - +
36r PHE* 4.2 21.7 - - + -
44r LEU* 3.7 5.3 + - + +
45r LEU* 1.3 73.7 - - - +
47r VAL* 1.3 73.1 + - - +
53r THR* 3.9 24.7 - - - +
56r PHE* 4.7 7.9 - - - -
57r ALA* 4.7 4.3 - - + -
100r VAL* 3.7 35.2 - - - -
101r ASN 3.8 4.0 - - - -
102r LEU* 4.2 9.2 - - + -
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Residues in contact with VAL 47 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1r MET* 5.1 5.6 - - - -
2r GLU* 3.4 47.6 - - + +
4r LEU* 3.6 34.8 - - + -
34r LYS* 4.0 6.3 - - + -
46r CYS* 1.3 81.9 - - - +
48r GLY* 1.3 64.9 + - - +
53r THR* 3.5 7.0 - - - -
100r VAL* 3.5 4.7 - - - -
101r ASN* 2.8 47.2 + - + +
132r HIS* 4.9 7.6 - - + -
133r GLY* 5.6 0.9 - - - +
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Residues in contact with GLY 48 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2r GLU* 3.0 25.4 + - - +
47r VAL* 1.3 79.3 - - - +
49r GLU* 1.3 68.6 + - - +
50r ALA* 3.8 0.5 + - - -
53r THR* 3.3 5.0 - - - +
99r HIS* 3.8 4.7 - - - -
101r ASN* 4.7 4.9 - - - -
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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