Contacts of the helix formed by residues 83 - 98 (chain B) in PDB entry 1YFL
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 SER 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B LYS 3.8 5.4 - - - -
79B LEU* 3.2 10.7 - - - +
80B SER* 2.4 53.9 + - - -
81B LYS 3.7 0.2 - - - -
82B THR* 1.3 63.2 + - - +
84B LYS* 1.3 63.2 + - - +
86B GLU* 3.2 32.0 - - - +
87B PHE* 3.2 18.4 + - - +
109B HIS* 5.6 0.5 + - - -
127B PHE* 3.7 7.5 - - - -
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Residues in contact with LYS 84 (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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82B THR 3.0 11.8 + - - +
83B SER* 1.3 73.0 - - - +
85B GLU* 1.3 67.3 + - + +
86B GLU* 3.5 0.8 + - - -
87B PHE* 3.1 5.0 - - - +
88B LEU* 3.1 47.5 + - + +
127B PHE* 3.8 35.9 - - + +
508F A 3.8 31.2 + - - -
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Residues in contact with GLU 85 (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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84B LYS* 1.3 82.3 - - + +
86B GLU* 1.3 79.1 + - - +
87B PHE 3.1 1.6 - - - -
88B LEU* 3.2 32.0 + - - +
89B LYS* 3.0 23.6 + - - +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 3.4 31.9 - - - +
78B LYS* 3.7 14.8 - - + +
79B LEU* 3.5 19.2 - - + +
83B SER* 3.2 23.8 - - - -
84B LYS 3.5 0.3 + - - -
85B GLU* 1.3 91.2 + - - +
87B PHE* 1.3 64.1 + - - +
89B LYS* 3.5 7.7 + - - +
90B LEU 3.2 14.0 + - - -
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Residues in contact with PHE 87 (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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79B LEU* 3.7 8.2 - - + +
83B SER 3.2 12.4 + - - +
84B LYS 3.1 11.2 - - - +
86B GLU* 1.3 74.9 - - - +
88B LEU* 1.3 71.7 + - + +
89B LYS 2.7 15.7 + - - -
90B LEU* 2.8 16.1 + - + +
91B ARG* 2.9 23.5 + - - +
106B LEU* 4.1 17.9 - - + -
109B HIS* 3.3 47.3 - + + -
110B GLY* 3.9 5.8 - - - -
123B PHE* 4.2 10.5 - + - -
125B THR 3.7 20.0 - - - -
126B PRO 3.9 2.7 - - - -
127B PHE* 3.1 44.4 - + + -
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Residues in contact with LEU 88 (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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84B LYS* 3.1 33.7 + - + +
85B GLU* 3.2 39.5 - - - +
87B PHE* 1.3 86.9 - - + +
89B LYS* 1.3 59.7 + - - +
91B ARG* 3.3 39.1 + - - +
92B GLU* 3.2 20.1 + - - +
507F G 6.4 1.1 - - - -
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Residues in contact with LYS 89 (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 TYR* 4.2 11.2 - - + -
85B GLU 3.0 11.5 + - - +
86B GLU* 3.5 11.2 - - - +
87B PHE 2.7 5.1 + - - -
88B LEU* 1.3 69.8 - - - +
90B LEU* 1.3 64.3 + - - +
91B ARG 2.9 3.8 - - - -
92B GLU* 2.8 21.6 + - - +
93B ASP* 2.8 19.8 + - - +
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Residues in contact with LEU 90 (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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73B VAL* 5.0 0.2 - - + -
77B TYR* 3.3 33.9 - - + +
79B LEU* 3.5 16.6 - - + -
86B GLU 3.2 4.5 + - - +
87B PHE* 2.8 14.1 + - + +
89B LYS* 1.3 75.0 - - - +
91B ARG* 1.3 63.4 + - - +
93B ASP* 4.0 0.9 - - - -
94B TYR* 3.1 14.9 + - - +
102B LEU* 3.3 41.1 - - + +
105B VAL* 3.4 37.0 - - + -
106B LEU* 3.8 19.6 - - + +
109B HIS* 4.9 1.3 - - + -
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Residues in contact with ARG 91 (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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87B PHE* 2.9 22.4 + - - +
88B LEU* 3.3 35.9 + - - +
89B LYS 2.8 0.8 + - - -
90B LEU* 1.3 75.0 - - - +
92B GLU* 1.3 67.9 + - - +
94B TYR* 2.7 15.4 + - - +
95B ASN* 2.8 28.4 + - - +
106B LEU* 3.6 12.3 - - + +
123B PHE* 3.6 37.3 + - + +
124B THR* 3.7 12.1 + - - +
125B THR 2.8 28.5 + - - -
126B PRO* 4.0 5.9 - - - +
507F G 3.4 29.9 + - - -
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Residues in contact with GLU 92 (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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88B LEU 3.2 8.6 + - - +
89B LYS* 2.8 15.7 + - - +
91B ARG* 1.3 74.8 - - - +
93B ASP* 1.3 64.8 + - - +
95B ASN* 3.0 13.9 + - + +
96B LYS* 2.7 61.3 + - + +
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Residues in contact with ASP 93 (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 TYR* 2.4 39.8 + - - +
89B LYS* 2.8 23.8 + - - +
90B LEU 3.7 6.3 - - - +
92B GLU* 1.3 74.0 - - - +
94B TYR* 1.3 63.7 + - - +
96B LYS* 3.2 8.5 + - - +
97B THR* 2.8 36.1 + - + +
102B LEU* 4.0 9.4 - - + -
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Residues in contact with TYR 94 (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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54B PRO* 3.7 17.3 - - - +
90B LEU 3.1 7.2 + - - +
91B ARG 2.7 14.5 + - - +
93B ASP* 1.3 70.6 - - - +
95B ASN* 1.3 64.8 + - - +
96B LYS 2.8 0.2 + - - -
97B THR* 4.0 4.0 - - - -
98B ARG* 2.5 61.6 + - - +
99B ASP 3.5 26.7 - - - -
100B PRO* 4.3 2.1 - - + +
102B LEU* 4.0 8.0 - - + +
103B LEU* 3.5 47.2 - - + +
106B LEU* 3.5 22.4 - - + -
117B ILE* 5.0 3.4 - - + -
121B GLY 4.9 5.4 + - - -
123B PHE* 3.7 28.9 - - + -
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Residues in contact with ASN 95 (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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91B ARG* 2.8 44.2 + - - +
92B GLU* 3.2 14.6 - - + +
94B TYR* 1.3 78.4 - - - +
96B LYS* 1.3 58.0 + - + +
98B ARG* 2.9 23.9 + - - +
122B ASN* 2.9 33.7 + - - +
123B PHE* 2.9 30.4 + - - +
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Residues in contact with LYS 96 (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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16A PRO* 6.3 3.6 - - - -
92B GLU* 2.7 61.4 + - + +
93B ASP* 3.7 8.7 + - - +
94B TYR 2.8 0.8 + - - -
95B ASN* 1.3 81.6 - - + +
97B THR* 1.3 69.0 + - + +
98B ARG* 3.5 5.5 + - - +
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Residues in contact with THR 97 (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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93B ASP* 2.8 31.4 + - + +
94B TYR 3.7 0.2 + - - -
96B LYS* 1.3 75.2 - - + +
98B ARG* 1.3 71.7 + - - +
99B ASP* 3.2 25.2 + - + +
102B LEU* 3.7 9.5 - - + +
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Residues in contact with ARG 98 (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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54B PRO* 6.2 1.2 - - - +
94B TYR* 2.5 43.8 + - + +
95B ASN* 2.9 27.3 + - - +
96B LYS 4.1 4.7 - - - +
97B THR* 1.3 76.0 - - - +
99B ASP* 1.3 57.9 + - - +
100B PRO* 3.0 16.1 - - - +
120B LYS 2.7 28.7 + - - -
121B GLY* 3.0 25.4 + - - -
122B ASN* 3.1 17.0 + - - +
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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