Contacts of the helix formed by residues 81 - 93 (chain Y) in PDB entry 6FF7
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 ASP 81 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80Y PRO* 1.3 77.5 - - - +
82Y SER* 1.3 61.4 + - - +
83Y LYS* 4.6 2.0 - - + +
84Y MET* 3.8 23.4 - - + +
85Y MET* 3.2 24.1 + - - +
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Residues in contact with SER 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y LEU* 3.7 38.4 - - - -
80Y PRO* 4.1 2.4 + - - +
81Y ASP* 1.3 70.1 - - - +
83Y LYS* 1.3 61.0 + - - +
85Y MET* 3.4 8.3 + - - +
86Y GLN* 2.9 27.8 + - - +
102Y MET* 6.0 1.2 - - - +
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Residues in contact with LYS 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y LEU* 5.6 0.4 - - - +
81Y ASP* 3.3 2.2 - - + +
82Y SER* 1.3 77.6 - - - +
84Y MET* 1.3 59.1 + - - +
86Y GLN* 3.2 8.3 + - - +
87Y ILE* 2.9 27.9 + - - +
2x THR* 5.8 8.5 - - - -
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Residues in contact with MET 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Y ASP* 3.6 23.9 + - + +
82Y SER 3.3 0.2 - - - -
83Y LYS* 1.3 74.8 - - - +
85Y MET* 1.3 59.7 + - - +
87Y ILE* 3.3 7.7 + - - +
88Y ASN* 2.9 30.7 + - - +
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Residues in contact with MET 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Y GLN* 5.8 8.3 - - + -
81Y ASP 3.2 15.6 + - - +
82Y SER* 3.5 12.3 - - - +
83Y LYS 3.3 0.2 - - - -
84Y MET* 1.3 76.8 - - - +
86Y GLN* 1.3 57.1 + - - +
88Y ASN* 3.4 5.1 + - - +
89Y LEU* 2.9 31.9 + - - +
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Residues in contact with GLN 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Y SER 2.9 17.0 + - - +
83Y LYS* 3.2 8.9 + - - +
85Y MET* 1.3 76.5 - - - +
87Y ILE* 1.3 58.1 + - - +
89Y LEU* 3.8 3.9 - - - +
90Y THR* 2.8 31.8 + - - -
98Y ALA* 4.4 8.7 - - + +
102Y MET* 5.4 12.8 - - + -
1x MET* 6.4 1.8 - - - -
2x THR* 6.1 4.9 - - - +
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Residues in contact with ILE 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83Y LYS 2.9 16.7 + - - +
84Y MET* 3.7 7.4 - - - +
85Y MET 3.3 0.2 - - - -
86Y GLN* 1.3 76.4 - - - +
88Y ASN* 1.3 57.1 + - - +
90Y THR* 3.2 6.7 + - - -
91Y GLY* 3.0 24.3 + - - -
607u ALA* 3.7 12.5 - - + +
6x THR* 5.5 11.9 - - - -
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Residues in contact with ASN 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Y MET 2.9 17.6 + - - +
85Y MET* 4.0 4.7 - - - +
87Y ILE* 1.3 77.1 - - - +
89Y LEU* 1.3 59.3 + - - +
91Y GLY* 3.9 1.4 + - - -
92Y PHE* 3.9 15.9 + - - +
607u ALA* 4.0 15.6 - - + +
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Residues in contact with LEU 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Y MET 2.9 18.6 + - - +
86Y GLN* 4.3 1.6 - - - +
88Y ASN* 1.3 75.5 - - - +
90Y THR* 1.3 63.8 + - - +
91Y GLY 3.3 0.4 - - - -
92Y PHE* 4.1 5.2 - - - +
93Y LEU* 3.3 26.9 + - - +
98Y ALA* 3.7 19.0 - - + +
101Y PHE* 6.1 2.5 - - + -
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Residues in contact with THR 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Y GLN 2.8 20.6 + - - -
87Y ILE* 3.2 6.9 + - - -
89Y LEU* 1.3 76.4 - - - +
91Y GLY* 1.3 57.7 + - - +
93Y LEU 3.0 22.5 - - - +
94Y ASN 4.5 2.1 - - - +
95Y GLY* 4.4 17.1 + - - -
98Y ALA* 3.9 10.3 - - - +
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Residues in contact with GLY 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87Y ILE 3.0 15.6 + - - -
88Y ASN 3.9 2.9 + - - -
89Y LEU 3.3 0.2 - - - -
90Y THR* 1.3 77.5 - - - +
92Y PHE* 1.3 60.8 + - - +
93Y LEU 4.0 1.7 - - - +
607u ALA* 4.4 17.5 - - - -
608u THR* 5.6 1.3 - - - -
611u SER* 3.5 17.0 - - - -
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Residues in contact with PHE 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Y ASN 3.9 13.8 + - - +
89Y LEU* 3.9 4.2 + - - +
90Y THR 3.4 0.2 - - - -
91Y GLY* 1.3 73.8 - - - +
93Y LEU* 1.3 68.4 + - + +
611u SER* 4.0 14.6 - - - -
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Residues in contact with LEU 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Y LEU 3.3 18.3 + - - +
90Y THR 3.0 14.2 - - - +
91Y GLY 4.0 2.4 - - - +
92Y PHE* 1.3 83.7 - - + +
94Y ASN* 1.3 64.3 + - - +
95Y GLY 3.4 4.0 - - - +
97Y ASN* 4.3 21.1 - - + -
98Y ALA* 4.7 4.3 - - + +
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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