Contacts of the helix formed by residues 91 - 105 (chain A) in PDB entry 1YKI
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LYS* 2.7 35.0 + - - -
89A ALA* 3.5 3.4 + - + +
90A MET* 1.3 74.5 - - - +
92A ASP* 1.3 63.3 + - - +
93A VAL* 3.5 15.1 + - + +
94A TRP* 3.1 31.3 + - - +
95A LEU* 3.3 14.6 + - - +
129A ARG* 3.8 5.4 - - - +
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Residues in contact with ASP 92 (chain A).
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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91A ASP* 1.3 70.6 - - - +
93A VAL* 1.3 66.8 + - + +
95A LEU* 3.2 7.0 + - - +
96A LYS* 2.9 24.3 + - - +
122A LYS* 3.9 15.0 + - - +
129A ARG* 2.9 35.4 + - - +
130A LYS* 5.9 0.5 + - - -
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Residues in contact with VAL 93 (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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91A ASP* 3.3 11.8 + - - +
92A ASP* 1.3 77.5 - - + +
94A TRP* 1.3 59.0 + - + +
96A LYS* 3.4 7.6 + - - +
97A LEU* 2.9 30.1 + - + +
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Residues in contact with TRP 94 (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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43A SER* 2.8 27.2 + - - -
44A GLN 3.3 19.8 + - - -
46A TRP 4.4 10.8 - - - -
87A LYS* 3.7 28.1 - - + +
90A MET* 3.9 19.7 - - + -
91A ASP* 3.1 29.3 + - - +
92A ASP 3.2 0.6 - - - -
93A VAL* 1.3 75.6 - - + +
95A LEU* 1.3 64.7 + - + +
97A LEU* 3.1 21.5 + - + +
98A VAL* 3.0 29.2 + - + +
183A TYR* 3.5 25.4 - - - -
208B LEU* 3.4 23.8 - - + -
212B ILE* 4.0 18.2 - - + -
213B THR* 4.8 1.3 - - + -
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Residues in contact with LEU 95 (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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43A SER* 5.5 2.9 - - - -
90A MET* 3.7 27.8 - - + -
91A ASP 3.3 8.4 + - - +
92A ASP* 3.2 10.0 + - - +
94A TRP* 1.3 76.9 - - + +
96A LYS* 1.3 61.4 - - - +
98A VAL* 3.5 4.3 + - + +
99A VAL* 3.2 23.7 + - - +
118A ASP* 4.7 4.9 - - - +
121A ARG* 3.7 35.8 + - + +
122A LYS* 3.7 32.8 - - + +
125A ALA* 4.0 14.8 - - + -
129A ARG* 3.8 31.9 - - - +
138A TRP* 5.8 0.7 - - + -
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Residues in contact with LYS 96 (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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92A ASP 2.9 16.3 + - - +
93A VAL* 3.6 8.5 - - + +
95A LEU* 1.3 75.0 - - - +
97A LEU* 1.3 59.4 + - - +
99A VAL* 4.0 11.1 - - + +
100A ASP* 2.6 69.8 + - - +
114A LYS* 3.9 14.5 - - - +
118A ASP* 5.3 2.0 - - - +
122A LYS* 5.7 0.4 - - - +
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Residues in contact with LEU 97 (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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93A VAL* 2.9 18.3 + - + +
94A TRP* 3.1 39.0 + - + +
96A LYS* 1.3 77.5 - - - +
98A VAL* 1.3 61.0 + - - +
100A ASP* 3.9 4.9 - - + +
101A GLN* 3.1 24.1 + - - +
208B LEU* 3.8 26.2 - - + -
212B ILE* 4.2 27.1 - - + -
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Residues in contact with VAL 98 (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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42A ASN* 3.3 24.2 - - + +
43A SER* 3.7 25.6 - - - +
44A GLN* 4.4 5.2 - - - +
94A TRP* 3.0 29.0 + - + +
95A LEU* 3.8 5.6 - - - +
96A LYS 3.3 0.2 - - - -
97A LEU* 1.3 76.8 - - - +
99A VAL* 1.3 57.5 + - - +
101A GLN* 3.3 3.8 + - - +
102A GLU* 3.0 30.3 + - + +
121A ARG* 3.7 31.9 - - - +
208B LEU* 4.2 19.3 - - + -
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Residues in contact with VAL 99 (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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95A LEU 3.2 9.0 + - - +
96A LYS* 3.4 23.8 - - + +
98A VAL* 1.3 78.4 - - - +
100A ASP* 1.3 68.9 + - - +
102A GLU* 3.3 4.2 + - - +
103A ASP* 3.0 27.5 + - - +
108A PHE* 3.6 15.4 - - + -
114A LYS* 4.0 23.3 - - + +
117A ASN* 3.5 21.5 - - - +
118A ASP* 4.1 18.2 - - + +
121A ARG* 3.6 14.1 - - - +
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Residues in contact with ASP 100 (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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96A LYS* 2.6 61.6 + - - +
97A LEU* 3.9 5.7 - - + +
99A VAL* 1.3 77.4 - - - +
101A GLN* 1.3 55.1 + - - +
103A ASP* 3.4 3.3 + - - +
104A ALA* 2.9 27.4 + - - +
114A LYS* 3.0 18.4 + - - +
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Residues in contact with GLN 101 (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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44A GLN* 5.9 0.4 - - - +
97A LEU* 3.1 16.9 + - + +
98A VAL 3.3 5.1 + - - +
100A ASP* 1.3 76.0 - - - +
102A GLU* 1.3 63.8 + - - +
104A ALA* 3.2 11.5 + - - +
105A ASP* 3.0 54.8 + - - +
206B SER* 3.5 8.1 - - - +
207B ARG 3.4 29.6 + - - +
208B LEU* 4.0 12.2 - - + +
209B PRO* 3.4 21.3 - - - +
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Residues in contact with GLU 102 (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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42A ASN* 3.0 34.1 + - - +
98A VAL* 3.0 18.1 + - - +
99A VAL* 3.3 7.1 + - - +
101A GLN* 1.3 75.8 - - - +
103A ASP* 1.3 59.2 + - - +
105A ASP* 3.3 1.7 + - - -
106A GLY 3.3 4.5 + - - -
107A ARG* 3.1 49.4 + - - +
108A PHE* 3.6 13.1 - - + -
117A ASN* 3.1 20.4 + - - +
121A ARG* 3.0 26.9 + - - -
206B SER* 3.2 21.8 - - - +
2218B FMN 4.5 3.3 + - - -
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Residues in contact with ASP 103 (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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99A VAL 3.0 13.7 + - - +
100A ASP 3.5 9.0 - - - +
102A GLU* 1.3 74.7 - - - +
104A ALA* 1.3 64.3 + - - +
106A GLY* 3.0 15.5 + - - +
107A ARG 4.7 0.9 - - - +
108A PHE* 3.6 28.7 + - + +
114A LYS* 2.9 36.2 + - - +
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Residues in contact with ALA 104 (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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100A ASP 2.9 16.7 + - - +
101A GLN* 3.2 18.8 + - - +
103A ASP* 1.3 76.1 - - - +
105A ASP* 1.3 62.4 + - - +
106A GLY* 3.2 1.3 + - - -
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Residues in contact with ASP 105 (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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101A GLN* 3.0 34.6 + - - +
102A GLU 3.7 5.6 - - - +
103A ASP 3.1 0.6 - - - -
104A ALA* 1.3 77.5 - - - +
106A GLY* 1.3 58.0 + - - +
107A ARG* 3.5 2.5 - - + -
204B PRO* 2.9 26.9 - - - +
205B LYS 3.9 12.1 - - - +
206B SER* 2.7 38.4 + - - -
207B ARG 3.8 3.1 + - - +
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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