Contacts of the strand formed by residues 1471 - 1475 (chain A) in PDB entry 5FLM
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 PHE1471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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875A TYR* 3.2 21.3 - - + +
1468A THR* 3.6 21.3 - - - -
1469A GLY 3.7 5.4 - - - +
1470A CYS* 1.3 81.2 - - + +
1472A ASP* 1.3 65.7 + - - +
1473A LEU* 3.6 21.5 - - + -
60F TYR* 4.0 2.5 - - + -
61F GLU* 3.5 37.7 - - + +
64F ARG* 3.4 62.3 + - + -
106F ILE* 3.7 23.6 - - + -
107F ARG 3.5 13.9 - - - +
108F ARG* 4.4 1.3 - - - +
109F TYR* 4.7 5.4 - - - -
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Residues in contact with ASP1472 (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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1471A PHE* 1.3 78.6 - - - +
1473A LEU* 1.3 88.1 + - - +
1474A LEU* 4.4 7.6 - - - +
64F ARG* 4.8 7.5 + - - +
106F ILE* 3.5 1.7 - - - -
107F ARG* 2.5 49.3 + - + +
109F TYR* 3.2 33.8 + - + +
58G VAL* 3.7 23.6 - - - +
59G ILE 4.3 4.5 - - - +
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Residues in contact with LEU1473 (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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1471A PHE* 3.6 20.4 - - + -
1472A ASP* 1.3 89.7 + - - +
1474A LEU* 1.3 65.2 + - - +
64F ARG* 3.7 31.6 - - + +
65F VAL* 3.7 13.9 - - + -
68F THR* 3.3 36.3 - - + +
104F ILE* 3.8 10.8 - - + -
105F ILE 4.0 0.9 - - - -
106F ILE* 3.6 29.6 - - + -
59G ILE* 3.3 36.1 + - + +
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Residues in contact with LEU1474 (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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1472A ASP* 4.4 4.7 - - - +
1473A LEU* 1.3 80.9 - - - +
1475A LEU* 1.3 60.5 + - - +
104F ILE* 3.3 6.8 - - - +
105F ILE* 2.8 63.7 + - + +
107F ARG* 3.3 54.5 - - + +
117F ASP* 4.2 6.3 - - - +
56G ALA* 4.6 9.4 - - + +
57G GLY 3.2 9.2 - - - +
58G VAL* 3.4 34.1 - - + -
59G ILE* 3.2 6.5 - - - -
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Residues in contact with LEU1475 (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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1474A LEU* 1.3 72.0 - - - +
1476A ASP* 1.3 80.0 + - - +
1477A ALA* 3.5 3.8 + - - +
1480A CYS* 3.7 8.3 - - - -
72F GLN* 4.3 11.4 - - - +
103F PRO* 4.0 12.3 - - + +
104F ILE* 5.3 1.1 - - + -
105F ILE* 4.8 4.0 - - - +
18G PHE* 3.8 43.3 - - + -
22G LEU* 3.5 16.2 - - + -
56G ALA* 5.5 1.7 - - - +
57G GLY 2.9 26.1 + - - +
59G ILE* 3.3 10.2 - - + +
66G VAL* 4.3 13.7 - - + -
68G TYR* 3.5 21.7 + - - +
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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