Contacts of the helix formed by residues 89 - 97 (chain A) in PDB entry 1YCH
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 ALA 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 3.4 15.8 + - - +
53A VAL 3.0 20.0 + - - +
55A GLU* 4.7 1.8 - - - +
58A LYS* 3.9 31.4 - - + -
61A LEU* 4.5 7.2 - - + -
87A ALA 3.2 0.8 - - - -
88A GLY* 1.3 76.7 - - - +
90A PHE* 1.3 65.0 + - - +
91A PRO* 3.4 2.5 - - - -
92A ALA* 3.4 6.8 + - + +
93A ILE* 3.0 24.9 + - + +
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Residues in contact with PHE 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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52A THR* 3.8 8.9 + - + -
77A LEU* 3.3 22.2 - - + -
79A VAL* 4.3 14.6 - - + -
87A ALA* 3.0 23.1 + - + +
89A ALA* 1.3 74.8 - - - +
91A PRO* 1.3 73.1 - - + +
93A ILE* 3.2 2.2 + - - +
94A MET* 2.9 56.2 + - + +
102A VAL* 3.9 16.6 - - + -
112A LEU* 3.9 23.8 - - + -
116A TYR* 3.9 26.0 - + + -
119A ILE* 4.5 14.1 - - + -
121A PHE* 4.1 22.4 - + - -
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Residues in contact with PRO 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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87A ALA 4.2 0.2 - - - +
88A GLY 3.7 12.3 - - - +
89A ALA 3.7 2.0 - - - -
90A PHE* 1.3 94.4 - - + +
92A ALA* 1.3 56.6 + - - +
94A MET* 3.7 1.8 - - + +
95A GLU* 2.8 35.4 + - - +
116A TYR* 3.8 24.7 - - + -
119A ILE* 3.6 29.5 - - + +
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Residues in contact with ALA 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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58A LYS* 3.8 35.0 - - + +
62A ILE* 4.4 16.3 - - + +
89A ALA* 3.4 8.9 + - - +
90A PHE 3.2 0.6 - - - -
91A PRO* 1.3 81.3 - - - +
93A ILE* 1.3 64.5 + - + +
95A GLU* 3.9 13.2 - - - +
96A LEU* 3.1 23.0 + - - +
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Residues in contact with ILE 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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49A LEU* 4.2 9.2 - - + -
52A THR* 3.9 18.8 - - + -
61A LEU* 4.4 10.8 - - + -
62A ILE* 4.1 19.3 - - + -
65A LEU* 3.9 28.7 - - + -
74A LEU* 3.5 28.5 - - + -
77A LEU* 4.4 15.7 - - + -
89A ALA* 3.0 22.0 + - + +
90A PHE* 3.9 2.7 - - - +
92A ALA* 1.3 75.8 - - + +
94A MET* 1.3 61.5 + - + +
96A LEU* 2.9 25.8 + - + +
97A CYS* 2.9 14.4 + - + +
100A ALA* 5.7 0.9 - - + -
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Residues in contact with MET 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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77A LEU* 3.1 38.4 - - + -
90A PHE* 2.9 40.8 + - + +
91A PRO 3.7 3.8 - - - +
93A ILE* 1.3 78.6 - - + +
95A GLU* 1.3 57.2 + - - +
97A CYS 4.0 14.6 - - - +
98A PRO* 3.1 34.6 - - - +
100A ALA* 4.2 15.3 - - + +
102A VAL* 4.0 6.3 - - + -
119A ILE* 3.9 28.3 - - + -
120A ASP 4.7 2.7 - - - +
121A PHE* 4.2 20.2 - - + -
391D ARG* 3.7 9.4 + - - +
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Residues in contact with GLU 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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91A PRO* 2.8 18.8 + - - +
92A ALA* 4.0 12.3 - - - +
94A MET* 1.3 75.7 - - - +
96A LEU* 1.3 60.5 + - - +
97A CYS 3.4 0.2 - - - -
98A PRO* 4.1 12.2 - - - +
391D ARG* 5.1 2.9 - - - +
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Residues in contact with LEU 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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62A ILE* 4.9 17.3 - - + -
65A LEU* 5.3 1.1 - - + -
66A LYS* 5.0 13.2 - - - +
72A VAL* 3.0 55.0 - - + +
92A ALA 3.1 16.4 + - - +
93A ILE* 2.9 15.0 + - + +
95A GLU* 1.3 81.2 - - - +
97A CYS* 1.3 75.4 + - - +
98A PRO* 3.8 4.0 - - - +
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Residues in contact with CYS 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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72A VAL* 3.7 15.0 - - - -
73A LYS 4.0 3.1 - - - +
74A LEU* 3.7 31.9 - - + +
93A ILE 2.9 7.2 + - - +
94A MET* 3.3 10.2 - - - +
96A LEU* 1.3 104.1 - - - +
98A PRO* 1.3 66.0 - - - +
99A ASP* 3.0 17.1 + - - +
100A ALA* 3.0 27.2 + - + +
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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