Contacts of the strand formed by residues 54 - 60 (chain H) in PDB entry 6FI8
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 GLU 54 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8H LYS* 2.6 45.8 + - - +
52H ARG 4.1 1.2 + - - -
53H VAL* 1.3 73.5 - - - +
55H ILE* 1.3 68.2 + - - +
56H ILE* 3.4 14.7 + - + +
69H ALA* 3.2 4.2 - - - -
70H ASP* 2.9 40.4 + - + +
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Residues in contact with ILE 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G GLN* 3.6 33.6 + - - +
133G ASN 4.0 7.8 - - - +
44H ILE* 3.7 32.3 - - + +
45H GLN* 4.1 16.4 - - - +
48H ALA* 3.7 26.2 - - + -
53H VAL* 3.7 6.1 + - + -
54H GLU* 1.3 74.6 - - - +
56H ILE* 1.3 64.1 + - - +
57H GLU 3.8 15.5 - - - +
58H MET* 3.9 16.2 - - + -
67H ILE* 4.8 10.5 - - + -
68H LEU 3.8 3.8 - - - +
69H ALA* 4.5 0.7 - - - +
80H PHE* 5.0 2.7 - - + -
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Residues in contact with ILE 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G LEU* 5.2 2.2 - - + -
125G LYS* 3.7 32.8 - - - +
130G ASN* 3.5 6.8 + - - -
132G GLN* 3.3 9.7 + - - -
133G ASN 4.1 5.0 - - - +
18H LYS* 3.8 37.9 - - + -
54H GLU* 4.1 23.6 - - - +
55H ILE* 1.3 73.4 - - - +
57H GLU* 1.3 66.7 + - + +
68H LEU* 2.6 37.6 + - + +
69H ALA 4.4 0.2 - - - -
70H ASP* 4.4 10.3 - - + +
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Residues in contact with GLU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G LYS* 3.5 29.0 - - + +
128G ILE* 3.3 27.9 - - + +
130G ASN* 3.3 29.2 + - + +
132G GLN* 3.5 2.5 - - - +
202G CA 2.7 28.8 - - - -
55H ILE* 3.8 3.3 - - - +
56H ILE* 1.3 93.0 - - + +
58H MET* 1.3 62.0 + - - +
67H ILE* 3.4 1.1 - - - -
68H LEU* 2.8 39.4 + - + +
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Residues in contact with MET 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE* 4.6 0.4 - - - -
130G ASN* 3.2 5.9 + - - -
131G GLN* 3.1 28.7 + - - +
132G GLN* 3.7 7.7 - - + +
41H LYS* 3.7 44.7 - - + +
44H ILE* 3.7 26.2 - - + -
45H GLN* 3.4 31.0 - - + +
55H ILE* 3.9 15.7 - - + -
57H GLU* 1.3 77.6 - - - +
59H GLN* 1.3 62.9 + - - +
65H ILE* 4.1 18.6 - - + -
66H HIS 3.2 12.6 - - - +
67H ILE* 4.1 6.7 - - + -
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Residues in contact with GLN 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ILE* 3.6 17.2 - - + +
129G GLU* 2.6 52.7 + - - +
131G GLN* 3.5 18.2 - - - +
58H MET* 1.3 73.1 - - - +
60H THR* 1.3 73.4 + - - +
61H ASP* 4.6 9.6 - - - +
65H ILE* 3.2 3.2 - - - -
66H HIS* 2.7 47.1 + - + +
0L C 3.1 38.4 + - - +
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Residues in contact with THR 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G GLN* 3.1 18.5 + - - -
32H LEU* 4.5 12.6 - - + -
37H GLU* 3.1 38.5 + - + +
40H LEU* 4.2 16.2 - - + -
41H LYS* 3.2 18.7 + - + -
59H GLN* 1.3 79.7 + - - +
61H ASP* 1.3 61.9 + - - +
62H LYS 3.9 0.7 - - - -
64H HIS 3.6 5.2 - - - -
65H ILE* 3.8 28.7 - - + -
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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