Contacts of the strand formed by residues 89 - 93 (chain A) in PDB entry 5FDK
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 TYR 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU 5.6 0.3 + - - -
36A GLU* 5.1 5.0 - - - +
39A LEU* 3.9 30.7 - - + +
40A ASN* 4.4 10.8 + - + +
43A ASN* 4.1 22.9 - - - -
54A ILE* 5.3 0.9 - - + -
55A HIS 3.7 5.6 - - - -
56A LYS* 3.2 62.8 + - + +
87A THR 4.2 1.7 - - - +
88A ASN* 1.3 85.7 - - + +
90A ASN* 1.3 65.1 + - - +
99A ASP* 3.3 4.9 - - - +
100A PHE* 2.9 74.5 + + + +
102A ALA* 4.4 9.4 - - + -
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Residues in contact with ASN 90 (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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54A ILE* 3.2 8.3 - - - +
55A HIS* 2.9 35.0 + - - +
57A LYS* 3.1 36.1 - - + +
86A THR* 5.1 0.8 - - - +
89A TYR* 1.3 77.2 - - - +
91A GLY* 1.3 59.3 + - - +
97A TYR* 3.5 17.3 + - + +
98A ILE* 3.2 17.5 - - - +
99A ASP* 3.4 12.7 + - - +
100A PHE* 5.8 0.2 - - - -
90C ASN* 2.6 35.8 + - - +
91C GLY* 5.2 0.2 - - - -
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Residues in contact with GLY 91 (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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53A VAL 3.2 10.8 - - - -
54A ILE* 4.3 1.3 - - - -
90A ASN* 1.3 80.9 - - - +
92A ILE* 1.3 59.0 + - - -
97A TYR* 3.5 1.6 - - - -
98A ILE* 2.9 35.8 + - - -
97C TYR* 3.1 33.4 - - - -
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Residues in contact with ILE 92 (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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52A ALA* 3.1 8.2 - - - +
53A VAL* 2.9 44.8 + - + +
54A ILE* 5.5 0.4 - - - +
91A GLY* 1.3 74.1 - - - -
93A TYR* 1.3 60.4 + - - +
95A GLY* 5.1 2.0 - - - +
96A ARG 3.4 6.5 - - - +
98A ILE* 4.4 2.0 - - - -
97C TYR* 4.1 24.1 - - + -
127C VAL* 5.5 6.7 - - + -
130C GLN* 4.6 24.2 - - + +
132C GLY* 5.5 1.3 - - - -
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Residues in contact with TYR 93 (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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51A ILE* 3.1 42.5 - - + +
52A ALA* 3.7 11.4 - - + -
92A ILE* 1.3 73.7 - - - +
94A LYS* 1.3 98.6 + - + +
95A GLY 3.1 0.7 - - - -
96A ARG* 2.8 24.6 + - - +
98A ILE* 4.1 18.6 - - + +
190A ILE* 4.2 22.9 + - + +
193A ILE* 5.2 9.2 - - + -
194A GLU* 2.3 45.2 + - + +
198A PHE* 4.1 17.0 - + - -
130C GLN* 4.4 3.1 - - - +
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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