Contacts of the strand formed by residues 66 - 70 (chain D) in PDB entry 5FLZ
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 66 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.9 2.2 - - - -
7D THR* 3.1 24.0 - - - +
9D GLN* 3.9 4.7 - - - +
22D TRP* 3.6 26.7 - - + +
64D PRO* 3.4 8.0 + - + +
65D ARG* 1.3 75.8 - - - +
67D ILE* 1.4 59.8 + - - +
68D MET* 5.6 4.5 - - + -
91D ASN* 3.1 29.3 + - - +
126D GLU* 4.5 2.4 + - - -
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.7 6.2 - - + +
7D THR 3.0 10.5 + - - +
8D LEU* 3.8 32.5 - - + -
9D GLN* 3.0 28.9 + - - +
66D ALA* 1.4 72.0 - - - +
68D MET* 1.3 63.1 + - - +
69D MET* 4.1 11.7 - - + -
91D ASN* 3.4 21.5 - - + +
119D ILE* 4.0 9.0 - - + +
122D LYS* 3.1 37.5 - - + +
123D ILE* 3.3 30.7 - - + +
126D GLU* 5.3 3.1 - - + -
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLN* 3.7 12.6 - - + +
15D ASN* 3.6 51.8 - - - +
18D GLY 4.7 0.9 - - - -
19D LYS* 4.6 4.3 - - + +
22D TRP* 3.7 35.2 - - + +
66D ALA* 4.2 4.2 + - + -
67D ILE* 1.3 75.7 - - - +
69D MET* 1.4 64.4 + - - +
74D SER 5.9 0.4 - - - -
75D VAL* 4.5 15.9 - - + -
78D ASP* 5.8 5.6 - - + +
87D PHE* 4.5 20.2 - - + -
91D ASN* 3.2 12.4 + - + +
92D THR* 4.5 10.1 - - - +
93D TRP* 3.1 24.9 + - - +
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Residues in contact with MET 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.3 11.9 - - + -
9D GLN 2.9 33.3 + - - +
10D ALA* 3.4 13.8 - - + -
11D GLY 4.5 0.4 - - - -
15D ASN* 3.0 7.9 - - - +
67D ILE* 4.1 26.7 - - + -
68D MET* 1.4 77.7 - - - +
70D ASP* 1.3 66.2 + - - +
93D TRP* 3.7 31.9 - - + -
119D ILE* 3.8 28.0 - - + -
122D LYS* 6.2 0.4 - - + -
123D ILE* 5.7 0.9 - - + -
150D LEU* 3.8 15.3 - - + -
154D LEU* 3.3 35.2 - - + -
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Residues in contact with ASP 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY* 3.4 32.1 - - - +
12D GLN* 3.6 5.4 + - - +
15D ASN* 3.6 14.6 - - - +
69D MET* 1.3 78.6 - - - +
71D SER* 1.3 83.7 + - - +
73D PRO* 4.7 4.0 - - - +
74D SER* 3.7 18.5 + - - -
75D VAL* 5.2 0.2 - - + -
93D TRP* 3.2 34.6 + - - +
95D ALA* 3.3 5.3 + - - -
146D THR* 4.4 15.4 + - - +
150D LEU* 5.0 0.2 - - - +
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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