Contacts of the helix formed by residues 93 - 105 (chain A) in PDB entry 1Y8M
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 TYR 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.8 40.0 + + - -
91A GLY* 2.7 45.5 + - - -
92A GLU* 1.3 74.2 - - - +
94A SER* 1.3 56.1 + - - +
95A MET 3.3 0.2 - - - -
96A ALA* 4.1 9.9 - - + -
97A LYS* 2.8 33.3 + - - +
120A VAL* 4.0 11.7 - - + -
123A LYS* 2.8 48.2 + - + -
124A ILE* 3.3 31.9 - - + +
127A GLU* 6.5 0.4 - - + -
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Residues in contact with SER 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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92A GLU* 2.5 16.0 + - - -
93A TYR* 1.3 74.3 - - - +
95A MET* 1.3 85.6 + - - +
97A LYS* 3.9 9.1 - - - +
98A ARG* 3.3 31.4 + - - +
124A ILE* 4.5 3.6 - - - +
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Residues in contact with MET 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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87A CYS* 4.3 11.7 - - - -
92A GLU* 2.7 31.0 + - + +
94A SER* 1.3 87.0 - - - +
96A ALA* 1.3 66.4 + - - +
98A ARG* 3.2 22.2 + - - +
99A TYR* 2.9 58.2 + - + +
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Residues in contact with ALA 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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84A THR* 4.0 24.7 + - + +
87A CYS* 3.7 25.4 - - + +
88A TYR* 4.5 3.8 - - - +
92A GLU 3.3 2.6 + - - -
93A TYR* 4.1 9.9 - - + -
95A MET* 1.3 80.2 - - - +
97A LYS* 1.3 62.5 + - - +
99A TYR* 3.3 3.1 + - - -
100A VAL* 2.8 28.7 + - - +
120A VAL* 3.8 19.1 - - + -
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Residues in contact with LYS 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 TYR 2.8 22.1 + - - +
94A SER* 3.9 10.1 - - - +
96A ALA* 1.3 77.5 - - - +
98A ARG* 1.3 64.2 + - + +
100A VAL* 3.4 5.7 - - + +
101A ASP* 2.8 37.9 + - + +
117A LYS* 6.2 3.1 - - - -
120A VAL* 3.5 10.9 - - + +
121A GLU* 5.6 11.4 - - + -
124A ILE* 3.6 35.8 - - + +
125A GLN* 5.6 2.1 + - - +
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Residues in contact with ARG 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 SER* 3.3 19.9 + - - +
95A MET* 3.2 22.7 + - + +
97A LYS* 1.3 85.3 - - + +
99A TYR* 1.3 68.2 + - + +
101A ASP* 3.6 6.8 - - - +
102A THR* 3.3 24.3 + - - -
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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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66A THR* 4.6 14.6 - - + +
69A TYR* 5.8 9.2 - + - -
80A LEU* 3.5 45.7 - - + +
83A LEU* 4.2 33.0 - - + -
84A THR* 4.3 2.2 - - - +
87A CYS* 4.9 4.7 - - - -
95A MET* 2.9 58.8 + - + +
96A ALA* 3.9 3.6 - - - +
98A ARG* 1.3 79.5 - - + +
100A VAL* 1.3 66.6 + - - +
102A THR* 3.2 6.6 + - - -
103A LEU* 3.1 19.1 + - - +
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Residues in contact with VAL 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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80A LEU 5.1 0.4 - - - -
81A TYR* 5.9 0.4 - - + -
84A THR* 3.6 25.7 + - + +
96A ALA 2.8 23.1 + - - +
97A LYS* 3.4 12.6 - - + +
99A TYR* 1.3 73.9 - - - +
101A ASP* 1.3 62.2 + - - +
103A LEU* 3.1 10.3 + - + -
104A PHE* 2.8 30.4 + - - +
113A VAL* 4.6 14.4 - - + -
116A LEU* 5.0 4.9 - - + -
117A LYS* 3.8 48.2 - - + +
120A VAL* 4.8 3.6 - - + -
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Residues in contact with ASP 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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97A LYS* 2.8 28.1 + - + +
98A ARG* 3.6 7.8 - - - +
100A VAL* 1.3 80.3 - - + +
102A THR* 1.3 65.5 + - - +
104A PHE* 3.4 7.6 + - - +
105A GLU* 3.1 27.2 + - - +
117A LYS* 4.7 13.8 - - - +
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Residues in contact with THR 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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80A LEU* 4.7 16.4 - - + -
98A ARG 3.3 10.7 + - - -
99A TYR* 3.2 10.3 + - - -
101A ASP* 1.3 83.0 + - - +
103A LEU* 1.3 64.5 + - - +
105A GLU* 3.3 26.4 + - - +
106A HIS* 3.4 5.2 + - - +
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Residues in contact with LEU 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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7A TRP* 6.0 4.5 - - + -
77A ARG* 4.0 39.9 - - + +
80A LEU* 4.4 13.4 - - + +
81A TYR* 3.9 37.0 - - + -
99A TYR 3.1 9.4 + - - +
100A VAL* 3.1 12.9 + - + +
102A THR* 1.3 81.7 - - - +
104A PHE* 1.3 62.5 + - - +
106A HIS* 3.0 27.8 + - + +
107A GLU 4.4 0.2 + - - -
108A ARG* 5.2 2.9 + - - +
113A VAL* 4.1 23.3 - - + +
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Residues in contact with PHE 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 VAL 2.8 19.1 + - - +
101A ASP* 3.9 5.8 - - - +
103A LEU* 1.3 73.6 - - - +
105A GLU* 1.3 66.8 + - - +
107A GLU* 3.2 14.0 + - - -
108A ARG 4.5 11.3 + - - +
113A VAL* 4.2 23.2 - - + +
114A GLY* 4.8 17.5 - - - -
117A LYS* 4.1 31.2 - - + -
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Residues in contact with GLU 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 ASP* 3.1 16.3 + - - +
102A THR* 3.4 21.1 + - - +
103A LEU 3.1 0.4 - - - -
104A PHE* 1.3 78.0 - - - +
106A HIS* 1.3 53.9 + - - +
107A GLU* 2.3 34.1 + - - +
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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