Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 1Y8Q
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 ASN 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP 2.7 24.2 + - - -
68A HIS* 3.8 9.9 + - - +
69A GLU 3.4 13.6 + - - -
70A GLN* 4.1 7.2 - - + +
89A ARG* 1.3 77.7 - - - +
91A ARG* 1.3 53.7 + - - +
92A ALA* 3.1 12.1 + - - +
93A GLU* 3.0 39.6 + - - +
94A ALA* 2.8 35.2 + - - +
112A THR* 3.4 25.2 + - + +
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Residues in contact with ARG 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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44A LEU* 4.0 20.4 - - + +
45A LYS* 3.6 26.7 - - - +
67A ASP* 3.4 24.6 + - + +
69A GLU* 3.1 48.4 + - - +
70A GLN 3.9 10.4 + - - -
71A VAL* 3.7 28.6 - - + +
72A THR* 4.2 13.3 + - - +
75A ASP* 2.6 38.3 + - - -
82A ILE* 4.2 4.8 - - + +
89A ARG 3.5 2.8 + - - -
90A ASN* 1.3 69.2 - - - +
92A ALA* 1.3 64.6 + - - +
94A ALA* 3.0 4.2 + - - +
95A SER* 2.9 28.0 + - - -
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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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44A LEU* 4.6 8.7 - - + -
65A MET* 3.5 22.5 - - + +
67A ASP* 4.1 20.9 - - + +
90A ASN* 3.1 11.4 + - - +
91A ARG* 1.3 78.2 - - - +
93A GLU* 1.3 61.2 + - - +
95A SER* 3.1 16.5 + - - -
96A LEU* 3.1 10.7 + - - -
110A VAL* 3.3 26.0 - - + +
111A ASP 4.1 1.1 - - - +
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Residues in contact with GLU 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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89A ARG* 4.0 22.2 + - - +
90A ASN* 3.0 25.4 + - + +
92A ALA* 1.3 76.8 - - - +
94A ALA* 1.3 62.0 + - - +
95A SER 3.0 1.3 + - - -
96A LEU* 3.4 20.6 + - + +
97A GLU* 4.6 1.7 + - - +
110A VAL* 3.7 19.4 - - + +
112A THR* 3.6 20.3 - - - +
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Residues in contact with ALA 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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71A VAL* 4.1 11.0 - - + -
81A LEU 3.2 13.0 - - - +
82A ILE* 3.6 30.2 - - + -
83A ARG 4.5 1.7 + - - -
86A SER* 4.2 3.4 - - - -
89A ARG* 4.0 28.5 + - + +
90A ASN 2.8 20.8 + - - +
91A ARG 3.0 5.8 + - - +
93A GLU* 1.3 73.6 - - - +
95A SER* 1.3 59.1 + - - +
97A GLU* 5.2 2.2 + - - +
98A ARG* 5.5 1.0 + - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.3 8.7 - - - +
65A MET* 3.8 12.3 - - - -
79A GLN* 3.3 21.5 + - - -
81A LEU* 3.6 26.9 - - - +
82A ILE* 3.4 5.0 - - - +
91A ARG 2.9 14.6 + - - -
92A ALA 3.5 7.9 - - - -
93A GLU 3.0 0.2 - - - -
94A ALA* 1.3 79.6 - - - +
96A LEU* 1.3 65.7 + - - +
97A GLU 3.3 3.0 + - - -
98A ARG 3.4 2.3 + - - -
99A ALA* 3.0 22.7 + - - +
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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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65A MET* 3.7 6.7 - - - -
92A ALA 3.1 5.5 + - - -
93A GLU* 3.4 15.6 + - + +
95A SER* 1.3 76.0 - - - +
97A GLU* 1.3 59.0 + - - +
99A ALA* 3.7 0.3 - - - +
100A GLN* 2.8 40.0 + - + +
108A VAL* 3.5 37.5 - - + +
109A LYS* 6.0 0.2 - - - -
110A VAL* 3.5 32.3 - - + -
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Residues in contact with GLU 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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83A ARG* 4.5 23.7 + - - +
93A GLU 4.6 2.2 + - - +
94A ALA 5.2 2.2 + - - +
95A SER 3.3 1.0 + - - -
96A LEU* 1.3 81.6 - - - +
98A ARG* 1.3 67.5 + - + +
100A GLN* 3.3 3.2 + - - +
101A ASN* 3.0 37.2 + - - +
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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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80A PHE* 3.4 14.8 + - - -
81A LEU* 3.3 34.4 - - + +
83A ARG* 3.1 36.3 - - + +
94A ALA 5.5 0.9 + - - +
95A SER 3.4 2.0 + - - -
97A GLU* 1.3 76.7 - - + +
99A ALA* 1.3 62.1 + - - +
101A ASN* 3.4 14.2 + - - +
102A LEU* 3.5 17.2 + - - +
62B LEU* 6.0 1.2 - - - +
64B GLN* 5.8 1.6 + - - -
79B SER* 3.8 15.4 + - - -
82B GLN* 3.2 35.7 + - - +
83B PHE* 3.2 43.3 - - - +
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Residues in contact with ALA 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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56A ILE* 3.4 31.6 - - + +
65A MET* 3.5 26.7 - - + -
81A LEU* 4.0 18.9 - - + +
95A SER 3.0 19.2 + - - +
96A LEU 3.7 0.9 - - - +
98A ARG* 1.3 78.0 - - - +
100A GLN* 1.3 61.9 + - - +
102A LEU* 3.3 19.3 + - - +
108A VAL* 4.4 1.3 - - + -
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Residues in contact with GLN 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 LEU* 2.8 27.3 + - + +
97A GLU* 3.8 4.5 - - - +
99A ALA* 1.3 73.5 - - - +
101A ASN* 1.3 66.0 + - - +
102A LEU 3.3 0.9 + - - -
103A ASN 3.3 22.0 + - - +
104A PRO* 3.9 11.8 + - + +
106A VAL 2.7 23.4 + - - +
107A ASP* 4.5 0.7 - - - +
108A VAL* 3.2 41.0 + - + +
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Residues in contact with ASN 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 GLU* 3.0 34.2 + - - +
98A ARG* 3.9 8.7 - - - +
99A ALA 3.3 0.6 - - - -
100A GLN* 1.3 76.6 - - - +
102A LEU* 1.3 62.6 + - - +
103A ASN* 3.0 4.7 + - - -
104A PRO* 4.3 10.4 - - - +
64B GLN* 3.5 29.3 - - + +
66B LYS* 4.0 21.8 - - - +
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Residues in contact with LEU 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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18A GLN* 5.5 0.5 + - - -
53A LYS* 3.7 37.2 - - + -
56A ILE* 3.9 11.2 - - + -
57A LEU* 3.5 23.3 - - + +
80A PHE* 4.9 1.3 - - + -
81A LEU* 4.3 10.8 - - + -
98A ARG 3.5 13.7 - - - +
99A ALA* 3.4 20.0 - - - +
100A GLN 3.2 0.8 - - - -
101A ASN* 1.3 77.4 - - - +
103A ASN* 1.3 63.2 + - - +
104A PRO* 4.5 0.4 - - - +
57B LEU* 4.6 4.7 - - - +
61B PHE* 3.6 46.4 - - + +
63B PHE 5.6 1.0 - - - +
64B GLN* 4.2 9.2 + - - +
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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