Contacts of the helix formed by residues 37 - 45 (chain I) in PDB entry 1YV0
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 37 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33I ALA 2.4 26.5 + - - +
34I ALA* 3.3 18.4 - - - +
35I ALA 2.6 0.2 - - - -
36I LYS* 1.3 73.6 - - - +
38I VAL* 1.3 60.7 + - + +
40I LYS* 3.0 28.3 + - - +
41I GLN* 3.5 24.9 + - - +
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Residues in contact with VAL 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ALA 2.7 24.5 - - - +
35I ALA* 2.6 14.2 + - - +
37I GLU* 1.3 76.6 - - + +
39I GLU* 1.3 55.6 + - - +
40I LYS 2.5 14.7 + - - -
41I GLN* 4.4 2.0 - - + +
42I ASN* 2.7 66.0 + - - +
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Residues in contact with GLU 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ALA* 2.6 19.5 + - + +
36I LYS* 2.9 51.8 + - - +
38I VAL* 1.3 72.6 - - - +
40I LYS* 1.3 55.0 + - - +
42I ASN* 4.7 4.0 - - - -
43I TYR* 2.9 28.1 + - - +
221T TYR* 3.6 17.4 + - + +
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Residues in contact with LYS 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I LYS 3.4 15.8 + - - +
37I GLU* 3.0 28.9 + - - +
38I VAL 3.7 0.2 - - - +
39I GLU* 1.3 78.2 - - - +
41I GLN* 1.3 71.7 + - - +
42I ASN 2.5 3.2 + - - -
43I TYR* 2.4 32.9 + - - +
44I LEU* 2.9 13.0 + - + -
218T THR* 5.5 5.1 + - - -
221T TYR* 3.8 31.2 - - + -
222T ASP* 3.3 28.6 + - - -
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Residues in contact with GLN 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I GLU* 3.5 24.1 + - - +
38I VAL* 3.4 2.1 + - - -
40I LYS* 1.3 96.3 - - - +
42I ASN* 1.3 64.4 + - - +
44I LEU* 3.5 31.8 - - - +
45I ALA* 2.8 27.7 + - - +
214T TYR* 4.9 11.9 + - - -
218T THR* 5.6 1.8 + - - -
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Residues in contact with ASN 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I VAL* 2.7 54.4 + - - +
39I GLU* 4.6 3.8 - - - -
40I LYS 2.5 4.8 + - - -
41I GLN* 1.3 79.5 - - - +
43I TYR* 1.3 60.9 + - - +
44I LEU 3.0 1.9 + - - -
45I ALA* 3.3 18.1 + - - +
46I GLU* 4.4 6.2 + - - +
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Residues in contact with TYR 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I GLU 2.9 21.7 + - - +
40I LYS* 2.4 19.1 + - - +
42I ASN* 1.3 73.4 - - - +
44I LEU* 1.3 58.4 + - + -
46I GLU* 4.3 16.0 - - - +
47I HIS* 4.5 28.5 + + + +
221T TYR* 3.8 36.6 - + - +
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Residues in contact with LEU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I LYS* 2.9 8.4 + - + +
41I GLN* 3.6 42.0 - - - +
43I TYR* 1.3 80.4 - - + +
45I ALA* 1.3 54.6 + - - +
46I GLU 2.6 18.0 + - - -
47I HIS* 3.4 14.0 + - + +
48I SER* 4.1 16.4 + - - +
214T TYR* 4.7 22.9 - - + +
217T GLN* 5.6 12.6 - - + +
218T THR* 4.8 18.4 - - - +
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Residues in contact with ALA 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I GLN 2.8 21.0 + - - +
42I ASN* 3.3 12.1 + - - +
44I LEU* 1.3 72.1 - - - +
46I GLU* 1.3 58.2 + - + +
49I PRO* 2.8 32.1 - - - +
50I PRO* 4.0 5.7 - - + +
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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