Contacts of the helix formed by residues 83 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D LYS 3.4 21.1 - - - -
79D LEU* 3.0 13.0 - - - +
80D SER* 2.6 39.4 + - - -
82D THR* 1.3 72.5 + - - +
84D LYS* 1.3 51.3 + - - +
86D GLU* 3.3 25.4 - - - -
87D PHE* 2.5 35.7 + - - +
109D HIS* 5.1 0.5 + - - -
127D PHE* 3.9 4.4 - - - -
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Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D THR 2.4 24.2 + - - +
83D SER 1.3 66.4 - - - -
85D GLU* 1.3 63.6 + - + +
86D GLU* 3.7 0.4 + - - -
87D PHE* 2.9 8.6 - - - +
88D LEU* 2.7 53.3 + - + +
127D PHE* 3.7 34.7 - - + -
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Residues in contact with GLU 85 (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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84D LYS* 1.3 84.6 - - + +
86D GLU* 1.3 77.2 + - + +
88D LEU* 2.9 25.5 + - - +
89D LYS* 2.9 21.8 + - - +
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Residues in contact with GLU 86 (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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77D TYR* 3.3 24.9 - - + +
78D LYS* 3.5 16.6 - - + +
79D LEU* 3.7 4.7 - - + +
82D THR 4.7 0.3 - - - +
83D SER* 3.3 30.4 - - - +
84D LYS 3.7 0.2 + - - -
85D GLU* 1.3 85.4 + - - +
87D PHE* 1.3 63.0 + - - +
89D LYS* 3.1 9.1 + - - +
90D LEU* 3.1 23.6 + - - +
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Residues in contact with PHE 87 (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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79D LEU* 3.7 8.9 - - + +
83D SER 2.5 20.7 + - - +
84D LYS 2.9 9.9 - - - +
86D GLU* 1.3 74.6 - - - +
88D LEU* 1.3 72.3 + - + +
90D LEU* 3.2 5.4 + - + +
91D ARG* 3.0 40.2 + - - +
106D LEU* 4.1 20.6 - - + -
109D HIS* 3.6 33.4 - + + -
110D GLY* 4.2 4.3 - - - -
123D PHE* 4.4 7.4 - + - -
125D THR 3.9 12.6 - - - -
126D PRO* 3.6 17.9 - - + -
127D PHE* 3.1 49.6 - + + -
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Residues in contact with LEU 88 (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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84D LYS* 2.7 35.7 + - + +
85D GLU* 2.9 31.4 + - - +
87D PHE* 1.3 83.6 - - + +
89D LYS* 1.3 61.6 + - - +
91D ARG* 3.4 46.7 + - - +
92D GLU* 3.2 21.4 + - - +
127D PHE* 6.1 0.2 - - + -
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Residues in contact with LYS 89 (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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77D TYR* 4.2 14.3 - - + -
85D GLU 2.9 12.0 + - - +
86D GLU* 3.1 11.4 + - - +
88D LEU* 1.3 74.3 - - - +
90D LEU* 1.3 68.6 + - - +
92D GLU* 3.0 16.4 + - + +
93D ASP* 2.8 45.0 + - - +
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Residues in contact with LEU 90 (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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73D VAL* 4.6 0.9 - - + -
77D TYR* 3.5 40.5 - - + +
79D LEU* 3.5 28.9 - - + -
86D GLU 3.1 9.5 + - - +
87D PHE* 3.4 9.0 - - - +
89D LYS* 1.3 76.9 - - - +
91D ARG* 1.3 65.3 + - - +
93D ASP* 3.1 3.6 + - - +
94D TYR* 2.8 24.9 + - - +
102D LEU* 3.6 28.9 - - + -
105D VAL* 3.9 16.6 - - + -
106D LEU* 3.4 28.5 - - + +
109D HIS* 4.8 2.2 - - + -
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Residues in contact with ARG 91 (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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87D PHE* 3.0 19.6 + - + +
88D LEU* 3.4 38.3 + - - +
90D LEU* 1.3 80.5 - - - +
92D GLU* 1.3 59.4 + - - +
94D TYR* 3.1 4.0 + - - +
95D ASN* 2.4 36.0 + - - +
106D LEU* 3.6 13.4 - - + +
123D PHE* 3.6 43.3 + - + +
124D THR* 4.1 8.6 + - - +
125D THR 3.0 30.7 + - - -
126D PRO* 4.1 8.1 - - - +
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Residues in contact with GLU 92 (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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88D LEU 3.2 10.7 + - - +
89D LYS* 3.0 17.2 + - + +
91D ARG* 1.3 80.4 - - - +
93D ASP* 1.3 63.2 + - - +
95D ASN* 2.9 23.9 + - + +
96D LYS* 3.1 40.9 + - + +
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Residues in contact with ASP 93 (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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77D TYR* 2.7 40.9 + - - +
89D LYS* 2.8 37.7 + - - +
90D LEU 3.4 7.4 - - - +
92D GLU* 1.3 71.0 - - - +
94D TYR* 1.3 62.9 + - - +
96D LYS* 3.1 22.0 + - - +
97D THR* 3.0 32.9 + - + +
102D LEU* 4.5 6.3 - - + -
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Residues in contact with TYR 94 (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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54D PRO* 4.0 14.9 + - - +
90D LEU 2.8 16.0 + - - +
91D ARG 3.4 6.5 - - - +
93D ASP* 1.3 72.4 - - - +
95D ASN* 1.3 61.8 + - - +
97D THR* 4.1 4.7 - - - -
98D ARG* 2.6 62.7 + - - +
99D ASP 3.2 29.6 - - - -
100D PRO* 4.4 1.5 - - + +
102D LEU* 4.1 13.6 - - + +
103D LEU* 3.4 40.7 - - + +
106D LEU* 3.9 17.0 - - + -
117D ILE* 5.3 2.4 - - + +
121D GLY 4.7 6.3 + - - -
123D PHE* 4.0 33.4 - - + -
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Residues in contact with ASN 95 (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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91D ARG* 2.4 52.9 + - - +
92D GLU* 2.9 14.2 + - + +
94D TYR* 1.3 80.4 - - - +
96D LYS* 1.3 58.1 + - + +
98D ARG* 2.7 26.3 + - - +
122D ASN* 2.7 31.6 + - - +
123D PHE* 2.9 30.1 + - - +
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Residues in contact with LYS 96 (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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92D GLU* 3.4 36.6 + - + +
93D ASP* 3.1 26.5 + - - +
95D ASN* 1.3 79.8 - - + +
97D THR* 1.3 68.5 + - + +
98D ARG* 3.7 5.4 + - - +
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Residues in contact with THR 97 (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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93D ASP* 3.0 21.9 + - + +
94D TYR* 3.9 4.3 + - - -
96D LYS* 1.3 78.9 - - + +
98D ARG* 1.3 72.4 + - - +
99D ASP* 3.1 22.7 + - - +
102D LEU* 4.3 6.1 - - + +
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Residues in contact with ARG 98 (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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54D PRO* 6.3 0.8 - - - +
94D TYR* 2.6 54.6 + - + +
95D ASN* 2.7 23.5 + - - +
96D LYS 4.1 6.1 - - - +
97D THR* 1.3 75.0 + - - +
99D ASP* 1.3 64.1 + - - +
100D PRO* 3.1 12.1 - - - +
120D LYS 2.6 29.9 + - - -
121D GLY* 3.2 27.7 + - - -
122D ASN* 3.6 10.5 - - - +
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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