Contacts of the helix formed by residues 29 - 34 (chain W) in PDB entry 4E2I
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 GLU 29 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W GLU 3.7 12.3 - - - +
26W LYS* 3.6 31.6 - - - +
27W LEU 3.0 0.4 - - - -
28W VAL* 1.3 76.7 - - + +
30W LEU* 1.3 54.3 + - - +
31W CYS 3.1 0.7 - - - -
32W VAL* 3.0 7.5 + - - +
33W GLN* 2.8 48.4 + - + +
66W GLU* 5.4 6.0 - - - +
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Residues in contact with LEU 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W LYS* 4.0 4.5 + - + +
27W LEU* 3.0 39.5 + - + +
29W GLU* 1.3 79.2 - - - +
31W CYS* 1.3 59.2 + - - +
32W VAL 3.2 0.2 - - - -
33W GLN* 4.0 1.1 - - - -
34W TYR* 3.5 48.4 + - + +
35W GLY 4.0 0.9 + - - -
36W GLN* 4.0 6.4 + - - +
41W MET* 3.4 29.8 - - + +
62W LEU 4.7 7.6 - - - +
65W PHE* 3.7 20.4 - - + -
66W GLU* 3.5 38.1 - - + +
70W LEU* 4.5 2.9 - - + -
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Residues in contact with CYS 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3W ALA* 3.5 30.4 - - + +
8W LEU* 3.6 23.3 - - - -
27W LEU 3.3 16.2 - - - -
28W VAL* 3.6 2.0 - - - +
29W GLU 3.1 0.8 - - - -
30W LEU* 1.3 77.1 - - - +
32W VAL* 1.3 60.2 + - - +
35W GLY* 3.3 21.9 - - - -
36W GLN 3.2 25.1 - - - +
37W ASN* 5.1 0.9 - - - -
38W GLU* 4.4 8.5 - - - +
41W MET* 3.9 8.5 - - - -
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Residues in contact with VAL 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W MET 4.7 8.7 - - - +
2W SER* 4.5 26.9 - - - +
3W ALA* 4.9 0.4 - - + -
28W VAL* 3.2 19.7 - - + +
29W GLU* 3.0 7.5 + - - +
31W CYS* 1.3 82.1 - - + +
33W GLN* 1.3 71.9 + - - +
34W TYR 3.4 1.6 - - - -
35W GLY* 4.2 1.6 - - - -
76W LYS* 3.9 12.6 + - - +
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Residues in contact with GLN 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W GLU* 2.8 28.7 + - + +
30W LEU* 4.6 0.2 - - - -
32W VAL* 1.3 89.0 + - - +
34W TYR* 1.3 81.7 + - + +
66W GLU* 4.6 8.7 - - - +
74W LEU* 4.5 4.2 - - - +
76W LYS* 3.6 18.7 - - - +
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Residues in contact with TYR 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30W LEU* 3.5 39.1 + - + +
33W GLN* 1.3 89.9 - - + +
35W GLY* 1.3 63.3 + - - +
36W GLN* 3.4 21.0 + - + +
66W GLU* 3.8 31.8 + - - +
70W LEU* 3.5 45.0 + - + +
71W SER* 4.7 1.4 - - - -
73W ARG 5.2 0.2 - - - -
74W LEU* 3.5 43.2 - - + +
75W SER* 4.2 13.7 + - - +
76W LYS* 3.2 22.8 - - - +
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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