Contacts of the strand formed by residues 25 - 29 (chain I) in PDB entry 5IYB
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 TYR 25 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B LYS* 4.0 17.7 + - + +
306B ASP* 3.1 26.9 + - - +
309B PHE* 3.3 23.8 - + - -
23I MET* 3.1 39.5 - - + +
24I LEU* 1.3 84.0 - - - +
26I PRO* 1.3 79.9 - - + +
27I LYS* 4.6 0.5 - - - +
37I TYR* 3.2 6.7 - - - -
38I ALA* 3.0 33.1 + - - +
40I ARG* 3.1 50.0 - - + +
173S HIS* 6.3 2.0 - - + -
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Residues in contact with PRO 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A TRP* 3.7 22.7 - - + -
1280A ASP* 5.7 3.1 - - - +
1282A ASP* 4.1 24.6 - - - +
1286A ARG* 6.1 0.7 - - - +
24I LEU 4.7 0.7 - - - +
25I TYR* 1.3 100.4 - - + +
27I LYS* 1.3 63.9 + - - +
35I LEU* 3.8 11.9 - - + -
36I LEU 3.2 8.1 - - - +
37I TYR* 3.4 21.0 - - + -
53I ILE* 4.3 13.9 - - + -
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210A TRP* 4.8 5.4 - - - -
25I TYR 4.6 1.1 - - - +
26I PRO* 1.3 77.5 - - - +
28I GLU* 1.3 70.2 + - - +
29I ASP 3.9 0.2 + - - -
35I LEU* 3.6 7.7 - - - +
36I LEU* 2.9 53.0 + - + +
38I ALA* 4.0 27.4 - - + -
45I GLN* 3.1 28.7 + - - -
173S HIS* 6.4 2.0 - - + -
174S PHE* 6.6 0.4 - - + -
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A TYR* 2.4 44.9 + - - -
1179A PRO* 4.6 2.1 - - - +
1209A PRO* 3.1 32.5 - - - +
1210A TRP* 3.3 20.0 + - - +
27I LYS* 1.3 89.6 + - - +
29I ASP* 1.3 63.3 + - - +
30I LYS* 3.4 29.0 + - + +
34I ILE 4.5 1.6 - - - -
36I LEU* 5.1 0.7 - - - -
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Residues in contact with ASP 29 (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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1177A TYR* 3.3 11.4 + - - -
27I LYS 3.9 0.2 + - - -
28I GLU* 1.3 74.9 - - - +
30I LYS* 1.3 58.3 + - - +
31I GLU* 2.9 28.2 + - - +
32I ASN* 2.9 31.6 + - - -
33I ARG 3.7 5.0 + - - -
34I ILE* 3.3 39.7 + - + +
36I LEU* 4.4 11.8 - - + +
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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