Contacts of the strand formed by residues 57 - 66 (chain E) in PDB entry 5IXM
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 GLY 57 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E TYR* 4.2 2.3 - - - -
53E LEU* 4.0 2.4 - - - -
54E LEU* 2.9 35.8 + - - +
55E ALA 3.0 2.3 - - - -
56E PRO* 1.3 79.6 - - - +
58E SER* 1.3 58.5 + - - -
91E HIS* 3.3 13.8 - - - -
92E SER 3.3 12.1 - - - -
93E GLY* 3.6 7.2 - - - -
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Residues in contact with SER 58 (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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52E TYR 3.5 10.8 - - - -
53E LEU* 3.8 20.1 - - - +
57E GLY* 1.3 73.7 - - - -
59E GLY* 1.3 59.0 + - - +
91E HIS* 3.4 4.3 + - - -
92E SER* 2.9 38.3 + - - -
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Residues in contact with GLY 59 (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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51E ARG* 3.5 1.9 - - - +
52E TYR* 2.9 53.2 + - - +
58E SER* 1.3 75.3 - - - +
60E THR* 1.3 67.7 + - - -
90E GLY 3.0 13.9 - - - -
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Residues in contact with THR 60 (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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49E GLU* 3.5 25.8 - - + +
50E PHE 3.5 4.5 - - - +
51E ARG* 3.6 26.1 - - + +
52E TYR* 3.8 1.0 - - - -
59E GLY* 1.3 77.1 + - - -
61E MET* 1.3 71.1 + - - +
88E TYR* 3.4 15.1 - - + -
89E TRP* 3.5 0.2 - - - -
90E GLY* 2.9 37.5 + - - -
121E TYR* 3.7 9.9 - - + +
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Residues in contact with MET 61 (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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49E GLU* 3.5 1.4 - - - -
50E PHE* 2.9 58.1 + - + +
52E TYR* 4.2 9.6 - - + -
60E THR* 1.3 77.9 - - - +
62E ALA* 1.3 65.1 + - - +
87E TYR* 3.1 33.0 - - + +
88E TYR 3.2 6.3 - - - +
89E TRP* 3.4 40.2 - - + +
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Residues in contact with ALA 62 (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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48E ASN 3.2 11.4 - - - +
49E GLU* 4.6 3.4 - - + -
61E MET* 1.3 79.8 - - - +
63E LEU* 1.3 61.0 + - - +
64E ASP* 5.0 4.0 - - - +
86E LEU* 4.1 4.7 - - + -
87E TYR* 3.2 12.6 - - - -
88E TYR* 2.9 37.7 + - + -
121E TYR* 3.6 34.8 - - + +
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Residues in contact with LEU 63 (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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48E ASN* 2.9 53.1 + - + +
62E ALA* 1.3 75.3 - - - +
64E ASP* 1.3 72.6 + - - +
65E TRP* 5.1 7.9 - - + -
85E TRP* 4.9 8.3 - - + -
86E LEU 3.2 18.2 - - - +
87E TYR* 4.5 17.9 - - + -
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Residues in contact with ASP 64 (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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45E GLN* 4.2 6.2 - - - +
46E TRP 3.3 4.0 - - - +
47E GLN* 3.5 40.2 + - - +
48E ASN 3.9 3.3 + - - +
62E ALA* 5.0 3.3 - - - +
63E LEU* 1.3 83.4 + - - +
65E TRP* 1.3 61.8 + - - +
84E ARG 4.3 0.4 - - - -
85E TRP* 3.0 10.9 - - - +
86E LEU* 2.9 41.2 + - + +
113E TYR* 3.2 25.9 + - - +
118E THR 4.8 0.3 - - - +
119E SER* 4.5 13.3 - - - -
121E TYR* 6.0 2.2 - - - -
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Residues in contact with TRP 65 (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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45E GLN* 3.8 3.3 - - - +
46E TRP* 2.8 60.3 + + + +
48E ASN* 5.3 2.5 - - - +
63E LEU* 5.1 11.2 - - + +
64E ASP* 1.3 75.9 - - - +
66E LEU* 1.3 58.4 + - - +
67E PRO* 3.5 43.7 - - + +
83E THR* 3.1 37.8 + - + +
84E ARG 3.6 1.3 - - - -
85E TRP* 4.8 4.7 - - + -
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Residues in contact with LEU 66 (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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39E MET* 4.2 2.9 - - + -
42E ARG* 3.7 32.8 - - + +
43E GLY* 4.0 8.5 - - - -
44E LEU 3.5 37.9 - - - +
45E GLN* 3.6 18.2 - - + +
65E TRP* 1.3 72.7 - - - +
67E PRO* 1.3 67.0 - - + +
68E ASN 4.6 6.1 - - - +
69E ASP* 4.1 4.9 - - + +
82E ALA 3.2 3.6 - - - +
83E THR* 3.3 3.0 - - - -
84E ARG* 2.8 62.2 + - + +
117E LEU* 4.1 11.4 - - + -
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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