Contacts of the strand formed by residues 56 - 61 (chain H) in PDB entry 4F1E
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 ILE 56 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G ARG* 3.0 13.3 + - - -
97G ASN* 2.7 24.2 + - - +
99G GLY* 3.1 18.4 + - - -
46H ASN* 3.6 14.8 - - - +
49H ILE* 3.4 30.3 - - + +
50H GLN* 3.7 20.9 - - + +
53H ASN* 3.7 23.6 - - - +
55H LYS* 1.3 69.1 - - - +
57H VAL* 1.3 59.7 + - - +
58H HIS* 3.6 30.7 - - + +
75H TRP* 3.7 24.4 - - + -
80H PHE* 4.2 1.6 - - + -
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Residues in contact with VAL 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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100G PRO* 3.5 28.0 - - + +
102G ILE* 3.9 19.1 - - + -
53H ASN* 5.1 0.8 - - - +
55H LYS* 3.3 27.6 + - + +
56H ILE* 1.3 79.1 - - - +
58H HIS* 1.3 69.8 + - - +
63N GLU 4.3 4.3 - - - +
64N ASP* 3.3 27.4 - - - +
65N LEU* 3.5 13.9 + - - +
66N GLY* 3.7 26.5 - - - +
68N LYS 5.0 2.4 - - - +
69N ALA* 5.9 0.7 - - - +
82N PHE* 5.3 4.0 - - - -
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Residues in contact with HIS 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ARG* 3.1 26.2 + - - +
100G PRO 3.3 6.9 + - - +
101G LEU* 3.4 23.0 - - + +
102G ILE* 2.7 33.4 + - - +
50H GLN* 4.6 11.2 + - - -
56H ILE* 3.6 24.0 - - + -
57H VAL* 1.3 75.9 - - - +
59H ALA* 1.3 56.2 + - - +
60H PHE* 3.9 6.5 - - + -
80H PHE* 3.8 19.7 - + - -
81H PRO* 3.7 26.6 - - + +
64N ASP 4.4 0.7 - - - -
79N LYS* 5.2 4.6 + - - -
82N PHE* 4.2 27.3 - + - -
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Residues in contact with ALA 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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102G ILE* 3.3 17.0 - - + -
104G LYS* 5.3 1.1 - - - -
58H HIS* 1.3 74.5 - - - +
60H PHE* 1.3 61.4 + - - +
60N PHE* 3.3 37.2 - - + -
64N ASP* 3.5 30.0 + - + +
82N PHE* 3.3 26.3 - - + -
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Residues in contact with PHE 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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101G LEU* 3.9 22.0 - - + -
102G ILE 2.8 6.7 + - - +
103G ILE* 3.4 8.8 - - + -
104G LYS* 2.9 28.5 + - - +
58H HIS* 3.9 11.4 - + + -
59H ALA* 1.3 73.7 - - - +
61H ASP* 1.3 64.1 + - - +
64H ASP* 4.1 10.8 - - + -
65H LEU* 3.8 18.8 - - + -
71H TYR* 3.7 29.8 - + - -
81H PRO* 3.9 20.0 - - + -
82H PHE* 4.5 14.4 - + - -
60N PHE* 4.5 1.6 - - - -
79N LYS* 3.9 13.9 - - + -
80N PHE 4.2 12.1 - - - -
81N PRO* 4.3 3.4 - - + -
82N PHE* 3.5 33.4 - + - -
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Residues in contact with ASP 61 (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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104G LYS* 2.8 43.0 + - - +
106G LYS* 2.8 43.3 - - + +
60H PHE* 1.3 73.4 - - - +
62H MET* 1.3 59.4 + - - +
63H GLU* 3.1 12.6 - - - +
64H ASP* 2.9 38.3 + - - +
65H LEU* 3.5 5.7 - - - +
57N VAL 4.0 1.7 - - - +
58N HIS* 3.2 19.5 - - - -
59N ALA 4.7 0.7 + - - -
60N PHE* 4.4 2.5 - - - -
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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