Contacts of the strand formed by residues 26 - 30 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLU* 5.8 2.5 - - - -
100D SER* 6.1 1.3 - - - -
101D MET 3.1 12.6 - - - -
102D ALA* 3.9 10.8 - - - -
24E ILE* 3.2 12.9 - - - +
25E PHE* 1.3 87.0 - - - +
27E TYR* 1.3 61.2 + - - +
28E THR* 4.9 6.9 + - - -
39E ILE 5.2 0.3 + - - -
40E ILE* 3.3 3.5 - - - -
41E THR* 2.6 49.0 + - - +
76E TYR* 3.9 1.6 - - - -
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Residues in contact with TYR 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ARG* 4.7 1.6 + - - -
71D THR* 4.8 1.3 - - + -
99D ILE* 3.8 1.5 - - + +
100D SER* 3.4 1.6 - - - -
101D MET* 2.7 62.0 + - + +
26E SER* 1.3 74.5 - - - +
28E THR* 1.3 62.7 + - - +
29E GLU* 2.7 49.2 + - + +
38E ALA* 4.4 15.4 - - + +
39E ILE 3.7 1.8 - - - -
40E ILE* 3.9 16.8 - - + -
69E LYS* 3.7 18.3 + - - +
72E LEU* 4.1 8.1 - - + -
73E ARG* 3.7 41.2 - - + +
76E TYR* 3.7 26.8 - - + -
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASN* 5.1 2.1 - - - -
5D ILE* 3.9 34.5 + - + +
8D LEU* 5.9 2.5 - - + -
98D ALA* 5.2 1.8 - - + -
99D ILE 3.1 14.4 - - - +
100D SER* 3.4 16.3 - - - -
26E SER* 4.9 5.9 + - - -
27E TYR* 1.3 76.9 + - - +
29E GLU* 1.3 65.1 + - - +
30E SER* 5.9 1.8 - - - -
38E ALA* 3.2 5.7 - - - +
39E ILE* 2.8 58.0 + - + +
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA 4.7 0.9 - - - +
67D ARG* 3.2 30.5 - - - +
68D MET* 3.3 24.2 + - + +
71D THR* 2.7 31.4 + - - -
98D ALA* 3.2 5.1 - - - +
99D ILE* 2.9 46.8 + - + -
27E TYR* 2.7 35.9 + - + +
28E THR* 1.3 75.4 - - - +
30E SER* 1.3 63.0 + - - +
37E MET 3.4 9.0 - - - +
38E ALA* 4.6 3.4 - - + -
73E ARG* 4.1 0.9 + - - -
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Residues in contact with SER 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.7 23.1 - - - +
64D ALA* 4.2 4.9 - - - +
68D MET* 5.0 1.6 - - - -
97D ALA 3.4 5.6 + - - -
98D ALA* 3.7 7.6 - - - -
28E THR* 5.9 0.9 - - - -
29E GLU* 1.3 77.9 - - - +
31E LEU* 1.3 58.4 + - - +
32E ALA* 3.1 21.8 + - - +
35E ARG 2.7 24.6 + - - -
36E GLU* 3.3 18.7 - - - +
37E MET* 3.0 15.0 + - - +
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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