Contacts of the strand formed by residues 56 - 61 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ARG* 3.1 8.1 + - - -
97A ASN* 2.7 33.8 + - - +
99A GLY* 3.0 24.3 + - - -
46B ASN* 3.7 10.5 - - - +
49B ILE* 3.3 36.6 - - + +
50B GLN* 3.8 16.8 - - + +
53B ASN* 3.9 20.0 - - + +
55B LYS* 1.3 68.9 - - - +
57B VAL* 1.3 60.5 + - - +
58B HIS* 3.6 31.0 - - + +
75B TRP* 3.7 23.1 - - + -
80B PHE* 4.3 1.3 - - + -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PRO* 3.5 33.4 - - + +
102A ILE* 3.9 21.1 - - + -
53B ASN* 5.0 1.0 - - - +
55B LYS* 3.4 22.3 + - + +
56B ILE* 1.3 79.7 - - - +
58B HIS* 1.3 69.1 + - - +
59B ALA 4.3 0.5 + - - -
63L GLU 4.9 2.0 - - - +
64L ASP* 3.5 24.3 - - - +
65L LEU* 3.7 12.4 + - - +
66L GLY* 3.7 25.8 - - - +
68L LYS 4.9 2.9 - - - +
69L ALA* 5.8 1.0 - - - +
82L PHE* 5.2 4.0 - - - -
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Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 3.1 26.0 + - - +
100A PRO 3.4 5.9 + - - -
101A LEU* 3.5 23.1 - - + +
102A ILE* 2.8 33.1 + - - +
50B GLN* 4.6 11.8 + - - -
56B ILE* 3.6 23.6 - - + -
57B VAL* 1.3 77.3 - - - +
59B ALA* 1.3 55.2 + - - +
60B PHE* 3.9 7.2 - - + -
80B PHE* 3.7 21.5 + + - -
81B PRO* 3.8 24.9 - - + +
79L LYS* 6.0 0.6 + - - +
82L PHE* 4.1 28.3 - + + +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.3 20.0 - - + -
104A LYS* 5.1 2.5 - - - -
57B VAL 4.2 0.6 - - - -
58B HIS* 1.3 73.0 - - - +
60B PHE* 1.3 61.5 + - - +
60L PHE* 3.2 33.5 - - + -
64L ASP* 3.4 28.4 + - + +
81L PRO* 4.4 0.3 - - - +
82L PHE* 3.1 27.9 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.9 13.7 - - + -
102A ILE 2.8 6.3 + - - +
103A ILE* 3.4 8.0 - - + -
104A LYS* 2.9 29.6 + - - +
58B HIS* 3.9 19.3 - - + -
59B ALA* 1.3 73.0 - - - +
61B ASP* 1.3 70.6 + - - +
64B ASP* 4.1 10.1 - - + -
65B LEU* 3.9 11.9 - - + -
71B TYR* 3.7 29.8 - + - -
81B PRO* 3.8 18.6 - - + -
82B PHE* 4.4 13.5 - + - -
60L PHE* 4.7 1.3 - - - -
79L LYS* 3.7 6.7 - - + -
80L PHE 3.7 21.1 - - - -
81L PRO* 3.9 4.0 - - + -
82L PHE* 3.4 34.1 - + - -
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 2.8 41.1 + - - +
106A LYS* 2.9 43.9 - - - +
60B PHE* 1.3 71.8 - - - +
62B MET* 1.3 60.7 + - - +
63B GLU* 3.6 12.6 - - - +
64B ASP* 2.9 37.5 + - - +
65B LEU* 3.3 7.4 - - - +
57L VAL 4.2 1.4 - - - +
58L HIS* 3.2 21.5 - - - -
59L ALA 4.8 1.0 + - - -
60L PHE* 4.8 2.3 - - - -
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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