Contacts of the strand formed by residues 23 - 28 (chain I) in PDB entry 5A31
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 23 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU* 3.5 31.0 - - + -
21I GLN 3.9 6.3 - - - +
22I GLU* 1.3 69.8 - - - +
24I ILE* 1.3 62.7 + - - +
25I PHE 3.8 15.0 - - - +
26I LEU* 3.7 32.3 - - + -
37I LEU* 3.7 30.5 - - + -
38I ALA 4.0 0.4 - - - +
39I ASN* 3.9 18.8 - - + -
569I LEU* 4.0 3.6 - - - +
734I LEU* 4.1 16.7 - - + +
738I LEU* 3.4 36.1 + - - +
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Residues in contact with ILE 24 (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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22I GLU 3.5 4.0 + - - -
23I ILE* 1.3 71.0 - - - +
25I PHE* 1.3 63.2 + - + +
38I ALA* 2.9 35.0 + - + +
39I ASN 3.5 16.4 - - - +
40I THR* 4.0 20.9 - - + +
68I VAL 4.0 13.5 - - - +
69I THR* 5.6 6.7 - - - +
567I ARG* 3.2 35.2 - - + -
569I LEU* 3.0 34.4 - - + +
738I LEU* 5.4 1.1 - - + -
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Residues in contact with PHE 25 (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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23I ILE* 3.5 3.1 - - - -
24I ILE* 1.3 82.7 - - + +
26I LEU* 1.3 75.8 + - - +
27I VAL* 3.4 34.3 - - + -
37I LEU* 3.7 0.5 - - - +
38I ALA* 2.6 37.4 + - + +
69I THR 4.3 19.5 - - - +
70I CYS* 5.5 7.0 - - - -
71I LEU* 3.7 49.5 - - + +
569I LEU* 3.3 31.9 - - + -
570I PHE* 4.9 8.1 - + + -
571I LYS* 4.8 12.3 - - + -
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Residues in contact with LEU 26 (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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23I ILE* 3.7 16.2 - - + -
25I PHE* 1.3 86.7 - - - +
27I VAL* 1.3 69.9 + - - +
35I ILE* 4.5 11.2 - - + -
36I ALA 3.1 15.9 - - - +
37I LEU* 3.2 26.0 - - + +
52I PHE* 5.2 2.9 - - + -
569I LEU* 6.0 0.8 - - + +
571I LYS* 5.1 14.5 - - + +
722I VAL 6.1 0.4 - - - -
723I ALA* 4.1 24.3 - - + +
732I CYS* 4.6 15.5 - - - -
734I LEU* 4.6 16.8 - - + +
741I VAL* 4.7 13.2 - - + -
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Residues in contact with VAL 27 (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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25I PHE* 3.4 29.8 - - + -
26I LEU* 1.3 80.3 - - - +
28I TRP* 1.3 81.1 + - - +
35I ILE* 3.3 6.7 - - - -
36I ALA 2.8 38.2 + - - +
71I LEU* 4.8 8.7 - - + +
72I ALA* 6.0 0.7 - - - -
73I TRP* 3.5 22.4 + - + +
571I LYS* 6.2 1.8 - - + -
642I GLN* 5.9 5.8 - - - +
723I ALA* 5.4 2.7 - - - -
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Residues in contact with TRP 28 (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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27I VAL* 1.3 89.3 - - - +
29I SER* 1.3 72.7 + - - +
30I PRO* 3.6 1.2 - - - +
33I ASP* 2.9 30.7 - - - -
34I LEU 4.0 2.7 - - - -
35I ILE* 3.3 35.1 - - + +
49I LEU* 4.8 4.3 - - + -
73I TRP* 3.8 2.2 - - - +
642I GLN* 5.4 0.2 - - - -
723I ALA* 2.5 47.6 + - + +
724I GLY 3.1 24.5 - - - +
725I ASN* 3.7 12.1 - - + -
730I VAL* 3.6 30.3 - - + -
731I SER* 3.5 16.1 - - - +
732I CYS* 3.3 23.3 - - + +
743I VAL* 4.0 11.9 - - + -
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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