Contacts of the helix formed by residues 89 - 100 (chain A) in PDB entry 1YQL
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 THR 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ARG* 4.1 9.0 - - - +
87A ARG 4.8 1.6 - - - +
88A PRO* 1.3 76.1 - - - +
90A PRO* 1.3 76.5 - - - +
91A ASP* 3.6 7.9 + - - +
92A GLU* 2.9 41.7 + - - +
93A LEU* 2.9 22.4 + - - +
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Residues in contact with PRO 90 (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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88A PRO 4.6 0.9 - - - +
89A THR* 1.3 88.5 - - - +
91A ASP* 1.3 61.6 + - - +
93A LEU* 3.4 12.0 + - + +
94A GLU* 2.8 27.7 + - - +
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Residues in contact with ASP 91 (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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89A THR* 3.2 7.5 + - - +
90A PRO* 1.3 80.6 - - - +
92A GLU* 1.3 65.0 + - - +
94A GLU* 3.1 19.2 + - - +
95A ALA* 3.1 12.6 + - - +
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Residues in contact with GLU 92 (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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62A GLN* 3.7 21.4 + - - +
64A TRP* 3.6 23.6 - - + -
77A VAL* 3.6 6.5 - - - +
79A ARG* 2.8 41.3 + - - -
88A PRO* 3.2 5.7 - - - +
89A THR* 2.9 37.4 + - - +
91A ASP* 1.3 77.2 - - + +
93A LEU* 1.3 63.6 + - - +
95A ALA* 3.0 23.3 + - - +
96A VAL 3.2 4.3 + - - -
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Residues in contact with LEU 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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24A ALA* 3.7 27.4 - - + +
25A SER 4.1 11.2 - - - +
26A ILE* 3.6 32.6 - - + +
64A TRP* 4.4 2.2 - - + -
75A CYS* 3.8 24.5 - - + -
88A PRO* 4.0 18.6 - - + +
89A THR 2.9 19.6 + - - +
90A PRO* 3.6 8.5 - - + +
92A GLU* 1.3 73.2 - - - +
94A GLU* 1.3 61.2 + - - +
96A VAL* 3.0 8.7 + - - +
97A ARG* 2.9 25.9 + - - +
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Residues in contact with GLU 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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90A PRO 2.8 14.4 + - - +
91A ASP* 3.1 19.7 + - - +
93A LEU* 1.3 77.4 - - - +
95A ALA* 1.3 55.4 + - - +
97A ARG* 3.1 25.2 + - - +
98A LYS* 2.9 66.4 + - + +
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Residues in contact with ALA 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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59A LEU* 4.1 4.8 - - + +
60A ALA* 4.2 24.7 - - + -
64A TRP* 5.5 1.1 - - + -
91A ASP 3.1 9.0 + - - +
92A GLU* 3.0 14.9 + - - +
94A GLU* 1.3 76.6 - - - +
96A VAL* 1.3 57.2 + - - +
98A LYS* 3.3 10.2 + - - +
99A TYR* 2.9 28.4 + - - +
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Residues in contact with VAL 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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26A ILE* 3.7 18.4 - - + -
59A LEU* 4.0 21.5 - - + -
64A TRP* 3.6 44.0 - - + -
66A LEU* 4.7 3.1 - - + -
73A LEU* 4.3 4.0 - - + -
75A CYS* 4.0 12.1 - - - -
92A GLU 3.7 2.5 - - - +
93A LEU* 3.0 10.2 + - - +
95A ALA* 1.3 75.7 - - - +
97A ARG* 1.3 66.9 + - - +
99A TYR* 3.1 10.2 + - - +
100A PHE* 3.2 36.6 + - + -
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Residues in contact with ARG 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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26A ILE* 3.6 35.2 - - + +
27A PRO* 4.4 10.4 + - - +
93A LEU 2.9 9.5 + - - +
94A GLU* 3.5 28.8 + - - +
96A VAL* 1.3 76.5 - - - +
98A LYS* 1.3 57.2 + - - +
100A PHE 3.5 0.7 + - - -
101A GLN* 3.1 21.5 + - - -
102A LEU* 3.2 53.9 + - + +
103A ASP* 2.8 30.1 + - - +
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Residues in contact with LYS 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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94A GLU* 2.9 47.9 + - - +
95A ALA* 3.3 11.2 - - - +
96A VAL 3.1 0.2 - - - -
97A ARG* 1.3 74.9 - - - +
99A TYR* 1.3 64.6 + - - +
101A GLN* 3.0 20.1 + - - +
134A ARG* 3.9 9.8 - - - +
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Residues in contact with TYR 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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39A LEU* 4.9 0.2 - - + -
44A SER* 3.7 9.4 + - - -
47A TRP* 3.0 39.9 + + - -
58A VAL 5.2 3.6 + - - -
59A LEU* 3.9 26.7 - - + -
95A ALA 2.9 14.0 + - - +
96A VAL 3.1 7.8 + - - +
98A LYS* 1.3 75.8 - - - +
100A PHE* 1.3 76.7 + + - +
133A LEU* 3.2 43.3 - - + +
134A ARG* 2.9 49.9 + - - -
135A GLN* 4.5 11.0 + - + +
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Residues in contact with PHE 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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33A LEU* 3.7 23.6 - - + -
35A LEU* 3.9 23.1 - - + -
38A VAL* 5.1 0.7 - - + -
39A LEU* 4.1 12.3 - - + -
59A LEU* 4.7 0.7 - - + -
66A LEU* 3.7 31.6 - - + -
73A LEU* 4.6 10.1 - - + -
96A VAL* 3.2 36.1 + - + +
97A ARG* 5.3 0.4 - - - -
98A LYS 3.2 0.6 - - - -
99A TYR* 1.3 91.9 - + - +
101A GLN* 1.3 72.9 + - - +
102A LEU* 3.0 22.3 + - + -
131A ARG* 2.9 27.6 + - - +
132A LEU 4.0 1.7 - - - +
133A LEU* 3.5 25.1 - - + -
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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