Contacts of the strand formed by residues 41 - 47 (chain p) 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 41 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37p ILE* 3.0 25.2 + - + -
38p SER* 2.8 48.7 + - - +
39p PRO 3.5 0.2 - - - -
40p ASN* 1.3 91.7 - - - +
42p TYR* 1.3 68.4 + - - +
63p LEU* 4.5 2.7 - - + -
74p PRO* 4.1 11.0 - - + -
75p ARG 3.6 31.9 - - - +
76p VAL* 3.9 17.0 - - + -
79p ALA* 4.5 8.7 - - + -
100p LEU* 3.8 24.2 - - + -
101p GLY 3.4 12.3 - - - +
102p GLY* 4.2 0.7 - - - -
178p ILE* 4.7 0.2 - - - -
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Residues in contact with TYR 42 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14p LEU* 3.6 22.6 - - + +
34p ILE* 4.0 16.2 - - + -
35p HIS 3.2 20.9 - - - -
36p PHE* 3.6 40.7 - + + +
37p ILE* 4.3 2.2 - - - -
38p SER 4.3 3.8 - - - -
39p PRO 4.7 0.2 - - - -
41p ILE* 1.3 81.4 - - - +
43p CYS* 1.3 61.7 + - - +
100p LEU* 3.9 2.3 - - - +
101p GLY 2.9 30.9 + - - +
176p CYS* 3.8 15.7 - - - -
178p ILE* 4.0 12.9 - - + +
183p LEU* 3.7 34.8 - - + +
185p PHE* 4.1 22.3 - + - +
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Residues in contact with CYS 43 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34p ILE* 4.2 0.9 - - - -
35p HIS* 2.6 45.9 + - - +
37p ILE* 3.7 19.3 - - + -
42p TYR* 1.3 76.7 - - - +
44p CYS* 1.3 60.7 + - - +
56p THR* 3.8 15.3 - - - +
83p LEU* 5.1 1.1 - - - -
98p LEU* 3.8 38.1 - - - -
99p VAL 3.3 12.6 - - - -
100p LEU* 3.7 18.2 - - + -
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Residues in contact with CYS 44 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3p ILE* 3.7 26.6 - - + +
4p ALA 4.5 0.9 - - - -
14p LEU* 3.7 39.9 - - - -
15p GLY 4.0 13.9 - - - -
33p LYS 3.1 7.0 - - - +
34p ILE* 3.9 17.0 - - - +
35p HIS* 4.5 0.4 - - - -
43p CYS* 1.3 74.8 - - - +
45p GLY* 1.3 59.9 + - - +
98p LEU* 3.3 9.8 - - - +
99p VAL* 2.9 37.1 + - + -
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Residues in contact with GLY 45 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1p THR* 4.1 6.9 - - - +
3p ILE* 3.8 3.7 - - - +
33p LYS* 2.9 30.2 + - - +
35p HIS* 4.0 12.5 + - - -
43p CYS 3.9 0.6 + - - -
44p CYS* 1.3 75.0 - - - +
46p ALA* 1.3 61.3 + - - +
52p THR* 4.4 9.8 + - - -
97p ALA 3.5 5.2 - - - -
98p LEU* 4.0 9.4 - - - -
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Residues in contact with ALA 46 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1p THR* 3.7 25.1 - - + -
3p ILE* 3.7 14.2 - - + +
45p GLY* 1.3 74.5 - - - -
47p GLY* 1.3 62.9 + - - +
52p THR* 3.2 10.5 - - - +
97p ALA* 2.8 37.4 + - + +
128p GLY* 4.1 22.2 - - - +
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Residues in contact with GLY 47 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1p THR* 5.5 1.4 - - - +
46p ALA* 1.3 78.7 - - - +
48p THR* 1.3 65.6 + - - -
49p ALA* 3.2 6.4 + - - +
95p GLY 3.5 5.6 - - - -
97p ALA* 4.5 5.8 - - - -
128p GLY* 5.7 0.4 - - - -
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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