Contacts of the helix formed by residues 34 - 39 (chain A) in PDB entry 1U0E
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A ASP* 3.1 14.2 + - - +
33A PRO* 1.3 83.0 - - + +
35A ARG* 1.3 64.5 + - - +
36A PHE 3.3 1.8 - - - -
37A ASN* 2.9 37.2 + - - +
38A ASN* 2.9 39.0 + - - +
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Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.5 0.2 - - - +
28A LEU* 3.9 37.2 + - - +
29A PHE* 3.7 32.8 - - + -
32A ASP* 3.1 32.2 + - - +
33A PRO 3.3 1.6 - - - -
34A GLU* 1.3 77.3 - - - +
36A PHE* 1.3 65.1 + - - +
39A PHE* 3.0 53.6 + - + +
55A SER* 2.8 24.4 + - - +
57A ASN 2.8 29.1 + - - -
59A VAL* 2.9 30.5 + - - +
60A ASN* 4.7 2.2 - - - +
539B SER* 3.9 6.3 + - - +
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Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 5.7 0.2 - - - +
34A GLU 3.3 0.4 - - - -
35A ARG* 1.3 77.2 - - - +
37A ASN* 1.3 76.6 + - - +
38A ASN 3.2 0.3 + - - -
39A PHE 3.2 6.2 + - - -
40A SER* 2.7 45.3 + - - -
51A LEU* 4.0 19.3 - - + -
53A ASP* 3.5 38.8 - - + -
55A SER* 4.0 9.4 - - - -
539B SER* 3.1 37.2 + - - +
540B SER* 3.7 9.9 - - - +
543B GLY* 3.6 36.1 - - - -
544B LEU 4.2 1.1 - - - -
547B PHE* 5.8 0.2 - - + -
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO 5.1 2.1 - - - +
34A GLU* 2.9 39.0 + - - +
36A PHE* 1.3 97.4 - - - +
38A ASN* 1.3 66.1 + - - +
39A PHE 3.7 0.2 + - - -
40A SER* 4.1 12.5 + - - +
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 4.7 4.2 - - - +
34A GLU* 2.9 35.6 + - - +
35A ARG* 4.9 0.2 - - - -
37A ASN* 1.3 86.2 + - - +
39A PHE* 1.3 81.8 + - + +
40A SER 3.7 2.2 - - - -
54A TYR* 3.9 8.5 + - - -
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 4.6 7.6 - - - -
35A ARG* 3.0 52.2 + - + +
36A PHE 3.2 1.5 + - - -
38A ASN* 1.3 92.3 - - + +
40A SER* 1.3 60.4 + - - +
54A TYR* 3.0 55.1 + + + -
55A SER* 3.0 21.5 + - - -
59A VAL* 4.2 13.7 - - + -
60A ASN* 3.8 12.8 - - - -
61A LYS* 3.7 24.5 - - + -
64A MET* 3.8 22.2 - - + -
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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