Contacts of the strand formed by residues 26 - 30 (chain K) in PDB entry 1S5E
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 SER 26 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J GLU* 6.0 1.3 - - - -
100J SER* 6.1 1.3 - - - -
101J MET 3.2 13.9 - - - -
102J ALA* 4.0 10.5 - - - -
24K ILE* 3.1 17.1 - - - +
25K PHE* 1.3 85.5 - - - +
27K TYR* 1.3 61.0 + - - +
28K THR* 4.3 6.5 + - - -
39K ILE 5.2 0.3 + - - -
40K ILE* 3.3 4.2 - - - -
41K THR* 2.7 46.1 + - - +
76K TYR* 4.0 1.6 - - - -
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Residues in contact with TYR 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ARG* 4.5 6.6 + - - -
71J THR* 4.8 2.0 - - + -
99J ILE* 3.9 2.3 - - + +
100J SER* 3.4 1.0 - - - -
101J MET* 2.8 57.8 + - + +
26K SER* 1.3 74.3 - - - +
28K THR* 1.3 63.5 + - - +
29K GLU* 2.8 45.8 + - + +
38K ALA* 4.2 18.3 - - + +
39K ILE 3.8 1.8 - - - -
40K ILE* 4.0 16.4 - - + -
69K LYS* 3.8 15.1 + - - +
72K LEU* 4.1 8.3 - - + -
73K ARG* 3.8 43.0 - - + +
76K TYR* 3.8 26.1 - - + -
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Residues in contact with THR 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J ASN* 5.5 2.0 - - - -
5J ILE* 4.0 34.9 + - + +
8J LEU* 5.7 3.1 - - + -
98J ALA* 5.2 1.8 - - + -
99J ILE 3.1 14.8 - - - +
100J SER* 3.4 15.9 - - - -
26K SER* 4.8 6.4 + - - -
27K TYR* 1.3 78.7 + - - +
29K GLU* 1.3 66.1 + - - +
30K SER* 5.9 0.7 - - - -
38K ALA* 3.2 7.8 - - - +
39K ILE* 2.9 55.5 + - + +
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Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64J ALA 4.6 0.9 - - - +
67J ARG* 3.1 34.9 - - - +
68J MET* 3.2 30.9 + - + +
71J THR* 2.7 29.9 + - - -
98J ALA* 3.2 4.4 - - - +
99J ILE* 2.9 36.8 + - + -
27K TYR* 2.8 34.4 + - + +
28K THR* 1.3 77.3 - - - +
30K SER* 1.3 65.3 + - - +
37K MET 3.6 7.9 - - - +
38K ALA* 5.1 0.9 - - + -
73K ARG* 4.2 0.2 + - - -
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Residues in contact with SER 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LEU* 3.4 26.5 - - - +
64J ALA* 4.1 4.9 - - - +
67J ARG* 6.1 0.3 - - - -
68J MET* 5.2 0.7 - - - -
97J ALA 3.4 5.2 + - - -
98J ALA* 3.9 0.4 - - - +
28K THR* 5.9 1.1 - - - -
29K GLU* 1.3 80.6 - - - +
31K LEU* 1.3 56.6 + - - +
32K ALA* 3.1 23.4 + - - +
35K ARG* 2.8 25.7 + - - +
36K GLU* 3.4 18.0 - - - +
37K MET* 3.0 18.1 + - - +
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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
------------------------------------------------------------
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