Contacts of the strand formed by residues 37 - 42 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E HIS* 3.5 7.9 - - + +
10E ALA* 4.2 5.6 - - + -
26E LEU* 3.4 50.0 - - + +
29E TYR* 3.9 19.1 - - + -
30E GLU* 2.7 29.9 + - + +
36E GLU* 1.3 78.7 - - - +
38E SER* 1.3 63.1 + - - +
39E PHE* 3.2 31.9 - - - +
40E VAL* 4.0 11.7 - - + -
82E TYR* 4.1 21.5 - - + -
258E TYR* 4.2 6.1 - - + -
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Residues in contact with SER 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 3.5 27.4 - - - +
8E HIS 2.8 15.6 + - - -
9E ILE* 4.8 0.2 - - - -
36E GLU* 3.5 11.2 + - - +
37E ILE* 1.3 73.8 - - - +
39E PHE* 1.3 80.2 + - - +
82E TYR* 5.6 1.3 - - - +
83E LEU* 5.2 4.5 + - - +
121E ILE* 5.8 0.2 - - - +
122E ASN* 4.1 13.7 + - - -
263E LEU* 5.3 2.4 - - - +
266E LYS* 5.4 7.8 + - - +
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Residues in contact with PHE 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 3.8 14.4 - - - -
8E HIS 4.1 0.6 + - - -
9E ILE* 3.6 45.7 - - + -
10E ALA 3.2 21.7 + - - -
37E ILE* 3.2 6.7 - - - +
38E SER* 1.3 88.7 - - - +
40E VAL* 1.3 69.4 + - - +
41E ILE* 3.8 14.8 - - + -
82E TYR* 4.9 3.6 - - - -
83E LEU* 3.4 24.2 - - + +
85E LEU* 4.0 23.1 - - + -
121E ILE* 3.5 45.1 - - + -
122E ASN* 4.2 2.5 - - - -
124E LEU* 4.3 2.0 - - + -
126E ILE* 4.2 8.5 - - + -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 3.4 11.9 - - + +
12E VAL* 3.8 27.6 - - + -
22E MET* 5.0 0.7 - - - -
23E TYR* 5.0 0.7 - - + -
26E LEU* 4.0 22.7 - - + -
37E ILE* 4.0 9.2 - - + -
39E PHE* 1.3 80.6 - - - +
41E ILE* 1.3 67.7 + - - +
42E CYS* 4.2 10.5 - - - -
82E TYR* 3.6 25.8 - - + -
83E LEU 2.9 9.2 + - - +
84E THR* 4.1 11.9 - - + +
85E LEU* 2.8 32.7 + - - +
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Residues in contact with ILE 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 3.9 17.7 - - + -
10E ALA 2.9 9.1 + - - +
11E ILE* 3.5 15.4 - - + -
12E VAL* 2.9 29.2 + - - +
39E PHE* 3.8 20.2 - - + -
40E VAL* 1.3 78.0 - - - +
42E CYS* 1.3 67.1 + - - +
43E THR* 4.8 3.1 - - + -
85E LEU* 3.3 12.8 - - + +
126E ILE* 4.6 6.3 - - + -
176E ILE* 4.1 25.8 - - + -
178E LEU* 3.5 45.3 - - + -
227E ILE* 5.1 1.1 - - + -
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Residues in contact with CYS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E VAL* 3.5 11.4 - - - +
13E GLY 4.6 0.2 - - - +
15E VAL* 3.8 11.9 - - + -
22E MET* 3.8 25.6 - - - -
40E VAL* 4.2 2.5 - - - -
41E ILE* 1.3 80.1 - - - +
43E THR* 1.3 61.2 + - - +
44E GLY 3.3 4.4 + - - +
46E MET* 3.7 26.5 - - + -
84E THR* 3.6 27.6 - - - -
85E LEU 2.8 7.9 + - - -
86E PHE* 3.3 22.5 - - + -
87E ILE* 3.5 4.5 + - - +
178E LEU* 5.0 1.6 - - - +
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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