Contacts of the strand formed by residues 89 - 95 (chain E) in PDB entry 1CSE
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 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E ASN* 4.4 14.4 + - - -
26E VAL 2.8 14.5 + - - +
27E LYS* 3.4 9.9 - - - +
28E VAL* 2.9 27.4 + - - -
45E VAL* 4.3 12.5 - - - +
87E SER 3.8 0.7 + - - -
88E VAL* 1.4 71.2 - - - +
90E LEU* 1.3 60.0 + - - +
91E TYR* 3.6 22.0 - - - -
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Residues in contact with LEU 90 (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 VAL* 3.7 11.4 - - + +
30E VAL* 3.6 31.0 - - + -
35E ILE* 4.3 10.3 - - + -
42E LEU* 4.3 10.8 - - + -
43E ASN 3.5 21.9 + - - +
44E VAL* 3.5 13.7 - - + -
45E VAL* 2.9 34.3 + - - +
69E ALA* 4.1 19.7 - - + -
72E VAL* 5.0 2.5 - - + -
73E ALA* 3.8 26.9 - - + -
88E VAL* 3.5 13.3 + - + +
89E SER* 1.3 72.5 - - - +
91E TYR* 1.3 69.7 + - - +
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Residues in contact with TYR 91 (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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27E LYS* 3.8 21.8 - - + +
28E VAL 2.8 11.6 + - - +
29E ALA* 3.5 5.5 - - + -
30E VAL* 3.0 29.3 + - - +
35E ILE* 4.5 4.3 - - - -
45E VAL* 3.4 26.6 - - + +
46E GLY* 3.2 30.1 - - - +
47E GLY* 4.0 2.5 - - - -
89E SER* 3.6 26.2 - - - -
90E LEU* 1.3 77.0 - - - +
92E ALA* 1.3 60.6 - - - +
93E VAL* 3.9 0.7 - - + -
113E TRP* 4.0 16.2 - + + -
119E MET* 3.5 43.7 - - + -
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Residues in contact with ALA 92 (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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30E VAL 4.0 1.8 - - - -
34E GLY* 4.9 1.6 - - - -
35E ILE* 3.8 32.3 - - + +
44E VAL* 4.0 9.1 - - + +
46E GLY 3.0 6.3 + - - -
47E GLY* 3.1 2.9 - - - -
48E ALA 3.0 21.1 + - - -
57E TYR* 3.3 39.5 - - + +
58E ASN* 5.3 0.2 - - - -
91E TYR* 1.3 70.2 - - - +
93E VAL* 1.3 63.1 + - - +
94E LYS 3.8 0.7 - - - -
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Residues in contact with VAL 93 (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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29E ALA* 3.7 23.6 - - + -
30E VAL 2.9 9.8 + - - +
31E LEU* 3.4 14.4 - - + -
32E ASP 2.9 25.5 + - - -
34E GLY* 5.3 1.0 - - - -
48E ALA 3.2 10.1 - - - +
50E PHE* 4.0 11.0 - - + -
91E TYR 4.5 1.8 - - - +
92E ALA* 1.3 77.8 - - - +
94E LYS* 1.3 61.5 + - - +
95E VAL* 3.3 5.6 + - + +
110E GLY* 3.7 33.4 - - - +
113E TRP* 3.6 33.7 - - + -
114E ALA* 5.4 0.2 - - + -
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Residues in contact with LYS 94 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E ASP 3.3 8.1 - - - +
33E THR 3.4 20.4 + - - -
34E GLY* 3.6 8.5 - - - +
48E ALA 2.9 9.4 + - - +
49E SER* 3.8 18.4 - - - +
50E PHE* 2.8 31.0 + - - -
51E VAL* 3.7 8.7 - - + +
54E GLU* 2.9 47.6 + - + +
55E ALA 2.7 23.5 + - - +
57E TYR* 4.2 7.0 - - - -
59E THR* 2.8 26.2 + - - +
92E ALA 3.8 2.0 + - - -
93E VAL* 1.3 70.7 - - - +
95E VAL* 1.3 62.4 + - - +
96E LEU 3.7 14.6 - - - +
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Residues in contact with VAL 95 (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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31E LEU* 3.8 17.0 - - + -
32E ASP 2.9 21.2 + - - +
50E PHE* 4.3 2.5 - - + -
51E VAL* 3.4 12.6 - - - +
93E VAL* 3.3 13.0 + - + +
94E LYS* 1.3 78.5 - - - +
96E LEU* 1.3 72.5 + - + +
102E GLY* 4.1 9.4 - - - -
103E SER 4.7 1.2 + - - -
106E GLY* 3.7 29.6 - - - +
107E ILE* 3.9 28.5 - - + +
110E GLY* 3.9 20.4 - - - -
126E LEU* 4.1 5.8 - - + -
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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