Contacts of the strand formed by residues 96 - 99 (chain A) in PDB entry 1FLS
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 ALA 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ILE* 5.0 4.5 - - + -
61A MET 3.2 13.3 + - - +
62A ILE* 3.5 8.8 - - + -
63A SER 3.3 20.1 + - - +
84A HIS 3.6 6.1 - - - -
85A ALA* 4.5 2.7 - - + -
94A GLY 4.9 1.8 - - - +
95A ASP* 1.3 79.7 - - - +
97A HIS* 1.3 70.3 + - - +
98A PHE* 4.1 4.8 - - + -
120A GLU* 3.4 35.4 - - - +
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Residues in contact with HIS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 5.1 4.1 - - + +
63A SER* 3.5 19.5 - - - +
65A GLY* 5.4 3.8 - - - +
69A HIS* 3.1 16.5 + + + -
75A PHE* 5.0 1.6 - - + -
83A ALA* 3.1 22.7 - - - +
84A HIS* 3.1 27.9 + + + +
86A PHE* 5.1 2.9 - + - -
95A ASP* 3.6 24.4 + - + +
96A ALA* 1.3 87.1 - - - +
98A PHE* 1.3 67.9 + - - +
120A GLU* 4.5 0.2 - - - +
167A ZN 1.9 41.9 - - - -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.4 8.7 - + - -
62A ILE* 3.6 23.8 - - + -
63A SER 2.9 15.5 + - - +
64A PHE* 3.2 26.4 - + + -
65A GLY* 2.6 33.4 + - - +
75A PHE* 5.0 2.2 - - - -
82A LEU 3.9 2.9 - - - -
83A ALA* 4.0 4.0 - - + +
96A ALA* 4.1 3.4 - - + -
97A HIS* 1.3 79.3 - - - +
99A ASP* 1.3 62.5 + - - +
104A TRP* 3.7 22.0 - + + -
113A LEU* 3.6 25.6 - - + -
116A VAL* 3.8 18.6 - - + -
117A ALA* 4.2 9.0 - - - -
120A GLU* 2.9 42.8 - - - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.7 0.4 - - - -
65A GLY 3.8 3.6 - - - -
66A ILE* 5.7 0.4 - - - +
75A PHE* 2.6 45.8 - - + +
77A GLY 4.1 1.9 - - - +
81A LEU 2.3 27.2 - - - +
82A LEU 3.3 10.0 + - - +
83A ALA 4.4 0.2 + - - -
98A PHE* 1.3 73.4 - - - +
100A ASP* 1.3 55.4 + - - +
101A ASP* 3.2 7.1 + - + +
102A GLU* 3.0 25.8 + - + +
104A TRP* 2.4 34.6 + - - -
168A CA 3.0 13.2 - - - -
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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