Contacts of the helix formed by residues 38 - 42 (chain E) in PDB entry 1YFL
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 VAL 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E LYS* 4.1 12.8 - - + +
15E LEU* 5.8 8.7 - - + -
18E LEU* 6.2 1.3 - - + -
22E PHE* 5.4 5.4 - - + -
28E PHE* 3.7 32.1 - - + -
30E ASP* 3.5 10.1 + - - +
36E LEU 3.0 0.6 - - - -
37E SER* 1.3 87.2 - - - +
39E SER* 1.3 69.4 + - - +
41E ASN* 2.7 18.5 + - - -
42E VAL* 3.5 16.9 - - + +
169E TYR* 4.0 28.5 - - + -
303E SFG 4.0 13.0 - - - +
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Residues in contact with SER 39 (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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28E PHE* 5.6 0.4 - - - -
30E ASP* 2.7 36.1 + - - +
33E CYS* 3.8 2.1 - - - +
36E LEU* 3.6 21.0 + - - -
38E VAL* 1.3 78.9 - - - +
40E LEU* 1.3 62.7 + - - +
41E ASN 3.0 1.2 + - - -
42E VAL* 3.4 16.7 + - - +
46E VAL* 3.8 25.0 - - - +
48E ALA* 3.8 10.1 - - - +
149E LYS* 4.1 7.8 - - - -
150E ILE* 4.1 11.8 - - - +
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Residues in contact with LEU 40 (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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2E LEU 4.4 0.9 - - - +
3E GLY 4.0 4.9 - - - +
4E ALA* 3.8 34.1 - - + +
36E LEU* 3.0 24.2 + - + +
39E SER* 1.3 77.4 - - - +
41E ASN* 1.3 68.4 + - - +
42E VAL 3.7 0.2 - - - -
142E HIS* 4.1 9.0 - - + +
143E PHE* 3.6 46.0 - - + +
146E ASN* 3.3 58.7 + - + +
147E CYS 3.9 0.9 - - - +
149E LYS* 3.8 4.2 - - - -
150E ILE* 4.2 8.3 - - + -
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Residues in contact with ASN 41 (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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1E MET* 3.5 43.8 + - + +
2E LEU 3.1 21.4 + - - -
15E LEU* 5.6 4.3 - - + -
19E LYS* 3.1 24.4 + - - +
37E SER 2.7 27.9 + - - +
38E VAL* 2.7 12.0 + - - +
40E LEU* 1.3 73.8 - - - +
42E VAL* 1.3 66.0 + - + +
142E HIS* 2.6 29.2 + - - -
146E ASN* 5.0 2.0 + - - +
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Residues in contact with VAL 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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19E LYS* 5.0 7.6 - - + +
22E PHE* 4.5 12.6 - - + -
25E TYR* 4.0 7.0 - - - +
28E PHE* 4.0 38.6 - - + -
38E VAL* 3.5 18.6 - - + +
39E SER* 3.4 21.3 - - - +
41E ASN* 1.3 83.9 - - + +
43E ASN* 1.3 64.2 + - - +
46E VAL* 4.2 8.7 - - + -
149E LYS* 2.9 30.8 + - - +
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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