Contacts of the strand formed by residues 37 - 42 (chain C) in PDB entry 4PEI
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 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C HIS* 3.6 8.3 - - - +
10C ALA* 4.3 5.4 - - + -
26C LEU* 3.4 48.2 - - + +
29C TYR* 3.8 21.3 - - + -
30C GLU* 2.9 31.9 + - + +
36C GLU* 1.3 85.8 - - - +
38C SER* 1.3 64.8 + - - +
39C PHE* 3.4 28.0 - - - +
40C VAL* 4.1 7.4 - - + -
82C TYR* 3.9 22.4 - - + -
258C TYR* 4.6 4.5 - - + -
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Residues in contact with SER 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 3.4 27.1 - - - +
8C HIS 2.7 17.1 + - - -
9C ILE* 4.8 0.4 - - - -
36C GLU* 3.6 4.3 + - - +
37C ILE* 1.3 74.8 - - - +
39C PHE* 1.3 78.9 + - - +
82C TYR* 5.4 1.8 - - - +
83C LEU* 5.1 4.2 + - - +
122C ASN* 3.9 6.7 + - - -
263C LEU* 5.6 2.1 - - - +
266C LYS* 6.0 0.3 - - - -
403C GOL 3.3 32.4 + - - -
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Residues in contact with PHE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 4.0 11.4 - - - -
8C HIS 4.1 0.2 + - - -
9C ILE* 3.5 40.8 - - + +
10C ALA 3.0 22.9 + - - -
37C ILE* 3.4 7.3 - - - +
38C SER* 1.3 89.8 - - - +
40C VAL* 1.3 71.8 + - - +
41C ILE* 3.6 24.2 - - + -
82C TYR* 4.8 3.1 - - - -
83C LEU* 3.3 24.0 - - + +
85C LEU* 3.8 25.8 - - + -
121C ILE* 3.8 42.0 - - + -
122C ASN* 4.3 1.1 - - - -
124C LEU* 4.4 1.8 - - + -
126C ILE* 4.0 8.1 - - + -
403C GOL 4.5 0.4 - - - -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA* 3.4 11.4 - - + +
12C VAL* 4.1 14.4 - - + -
22C MET* 4.8 1.3 - - - -
23C TYR* 5.0 0.4 - - + -
26C LEU* 3.8 27.4 - - + -
37C ILE* 4.1 7.4 - - + -
39C PHE* 1.3 81.9 - - - +
41C ILE* 1.3 59.8 + - - +
42C CYS* 3.9 23.3 - - - -
82C TYR* 3.7 27.1 - - + -
83C LEU 2.8 9.5 + - - +
84C THR* 3.2 12.4 - - + +
85C LEU* 2.8 34.1 + - - +
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Residues in contact with ILE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 3.7 20.6 - - + -
10C ALA 2.8 10.3 + - - +
11C ILE* 3.5 14.8 - - + -
12C VAL* 2.8 33.8 + - - +
39C PHE* 3.6 23.8 - - + -
40C VAL* 1.3 73.4 - - - +
42C CYS* 1.4 58.0 + - - +
43C THR* 4.4 7.4 - - + -
85C LEU* 3.3 9.9 - - + +
126C ILE* 4.2 6.5 - - + -
176C ILE* 4.0 30.1 - - + -
178C LEU* 3.3 42.2 - - + -
227C ILE* 5.4 0.7 - - + -
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Residues in contact with CYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.5 7.9 - - - +
15C VAL* 3.8 22.7 - - + -
22C MET* 3.8 15.7 - - - -
40C VAL* 3.9 5.6 - - - -
41C ILE* 1.4 77.8 - - - +
43C THR* 1.3 63.8 + - - +
44C GLY 3.4 1.2 + - - -
46C MET* 3.6 26.5 - - + -
84C THR* 3.6 26.0 - - - -
85C LEU 2.8 7.9 + - - +
86C PHE* 3.2 24.6 - - + +
87C ILE* 3.4 5.0 + - - +
178C LEU* 4.9 0.7 - - - +
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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