Contacts of the strand formed by residues 75 - 79 (chain B) in PDB entry 6FEQ
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 LEU 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLY* 1.3 74.0 - - - +
76B ASN* 1.3 61.7 + - - +
77B ALA* 4.8 0.2 - - - +
225B LEU* 5.7 4.0 - - + +
228B LEU* 4.7 12.8 - - + +
229B LYS* 5.2 10.8 - - + +
232B SER* 4.8 3.8 - - - -
238B ILE* 3.7 27.8 - - + -
240B PHE* 3.5 28.7 - - + -
252B LEU* 3.5 26.5 - - + +
253B PHE* 3.6 24.0 - - + +
254B ASP* 3.1 26.0 + - - +
255B SER 2.9 27.9 + - - +
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Residues in contact with ASN 76 (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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71B MET* 3.5 45.4 - - + +
72B LYS* 3.1 23.7 + - - +
74B GLY 4.7 0.2 + - - -
75B LEU* 1.3 74.4 + - - +
77B ALA* 1.3 59.9 + - - +
78B ILE* 5.6 0.7 - - - -
237B THR* 4.7 2.8 - - - -
238B ILE 2.8 31.0 + - - +
239B ILE* 4.0 17.0 - - + +
240B PHE* 3.2 23.0 + - - -
255B SER* 3.4 25.7 + - - -
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Residues in contact with ALA 77 (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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71B MET* 6.0 0.5 - - - +
76B ASN* 1.3 74.8 - - - +
78B ILE* 1.3 66.5 + - - +
79B LEU* 4.2 2.9 - - + -
240B PHE* 3.6 17.5 - - + -
241B SER* 5.8 0.2 - - - -
242B ILE* 5.7 0.9 - - + +
253B PHE* 4.0 36.6 - - + -
255B SER 2.8 14.1 + - - +
256B LEU* 3.5 8.5 - - + -
257B THR* 2.8 26.0 + - - -
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Residues in contact with ILE 78 (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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71B MET* 4.5 17.5 - - + -
76B ASN 5.6 0.2 - - - -
77B ALA* 1.3 79.6 - - - +
79B LEU* 1.3 65.2 + - - +
86B LYS* 3.7 30.8 - - + +
89B LEU* 4.0 26.9 - - + -
90B LEU* 4.9 14.1 - - + +
93B LEU* 6.2 0.4 - - + -
239B ILE* 4.7 10.3 - - + -
240B PHE 3.0 17.5 + - - +
241B SER* 3.3 23.4 - - - +
242B ILE 3.6 5.2 + - - -
257B THR* 3.3 20.6 - - - +
259B LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 79 (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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77B ALA* 4.2 1.3 - - + -
78B ILE* 1.3 82.2 - - - +
80B GLY* 1.3 58.9 + - - +
86B LYS* 4.7 4.1 - - - +
242B ILE* 3.4 31.6 - - + +
245B PRO* 3.7 33.7 - - + -
250B PHE* 4.6 9.2 - - + -
253B PHE* 4.8 5.2 - - + -
256B LEU* 3.7 31.6 - - + +
257B THR 2.9 7.3 + - - +
258B LEU* 3.3 14.0 - - + +
259B LEU* 3.0 28.1 + - - +
291B ALA* 4.4 14.4 - - + +
294B PHE* 5.0 7.9 - - + -
295B LEU* 5.2 5.4 - - + -
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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