Contacts of the strand formed by residues 54 - 60 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G LYS* 2.7 40.6 + - - +
52G ARG 4.1 1.2 + - - -
53G VAL* 1.3 71.3 - - - +
55G ILE* 1.3 70.7 + - - +
56G ILE* 3.5 20.5 + - + +
69G ALA* 3.2 5.2 - - - +
70G ASP* 2.8 46.9 + - + +
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Residues in contact with ILE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ILE* 3.7 30.5 - - + +
45G GLN* 3.7 33.9 - - - +
48G ALA* 3.7 26.7 - - + -
53G VAL* 3.8 4.8 + - + -
54G GLU* 1.3 75.9 - - - +
56G ILE* 1.3 63.2 + - - +
57G GLU* 3.8 21.5 - - - +
58G MET* 3.9 18.2 - - + -
67G ILE* 4.9 10.8 - - + -
68G LEU 3.8 2.7 - - - +
69G ALA* 4.5 0.7 - - + +
80G PHE* 5.1 1.3 - - + -
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Residues in contact with ILE 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LYS* 3.7 43.3 - - + -
54G GLU* 3.5 26.4 + - + +
55G ILE* 1.3 73.1 - - - +
57G GLU* 1.3 59.8 + - - +
68G LEU* 2.7 36.2 + - + +
69G ALA 4.7 0.2 - - - -
70G ASP* 4.5 9.2 - - + +
121H LEU* 4.3 15.9 - - + -
125H LYS* 3.5 30.1 - - + -
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ILE* 3.4 6.3 - - - +
56G ILE* 1.3 76.1 - - - +
58G MET* 1.3 64.7 + - - +
59G GLN* 2.6 27.7 + - - -
66G HIS 4.6 0.2 - - - -
67G ILE* 3.6 0.5 - - - -
68G LEU* 2.7 47.6 + - + +
201G CA 2.5 32.1 - - - -
125H LYS* 2.8 42.5 + - + +
128H ILE* 3.6 27.6 - - + -
129H GLU* 3.0 13.5 - - + +
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Residues in contact with MET 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LYS* 3.6 53.2 + - + +
44G ILE* 3.6 29.2 - - + -
45G GLN* 3.6 26.7 - - + +
55G ILE* 3.9 14.3 - - + +
57G GLU* 1.3 82.0 + - - +
59G GLN* 1.3 75.3 + - - +
65G ILE* 4.1 21.1 - - + -
66G HIS 3.2 15.0 - - - +
67G ILE* 4.2 5.8 - - + -
128H ILE* 5.0 0.2 - - - -
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Residues in contact with GLN 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LYS* 4.2 13.8 + - - +
57G GLU* 2.6 27.2 + - - +
58G MET* 1.3 79.8 + - - +
60G THR* 1.3 65.2 + - - +
61G ASP* 5.5 2.5 - - - +
65G ILE* 3.6 1.0 - - - +
66G HIS* 2.7 44.1 + - + +
201G CA 4.3 3.0 - - - -
128H ILE* 3.5 35.3 - - + +
129H GLU* 3.8 15.9 + - - +
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Residues in contact with THR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 4.6 5.8 + - - -
37G GLU* 3.2 39.5 + - + +
40G LEU* 4.4 10.1 - - + -
41G LYS* 3.7 27.7 + - + +
58G MET* 5.1 0.4 - - + -
59G GLN* 1.3 80.0 + - - +
61G ASP* 1.3 71.7 + - - +
64G HIS 3.7 4.7 - - - -
65G 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