Contacts of the helix formed by residues 76 - 89 (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 ARG 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A TYR* 3.9 40.9 + - + +
73A GLU* 4.4 13.4 - - - +
74A SER* 2.7 24.7 + - - +
75A ARG* 1.3 76.8 - - - +
77A ARG* 1.3 66.0 + - - +
79A CYS* 3.0 5.8 + - - +
80A LEU* 2.7 48.8 + - + +
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Residues in contact with ARG 77 (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* 4.0 19.4 - - + -
74A SER* 3.5 31.5 + - - +
75A ARG 3.4 0.2 - - - -
76A ARG* 1.3 89.2 - - - +
78A GLU* 1.3 78.4 + - - +
80A LEU* 3.9 3.1 - - + +
81A TYR* 3.0 25.5 + - - +
103A LEU* 4.0 26.5 - - + +
106A HIS* 5.4 12.2 - - + +
108A ARG* 5.1 16.1 - - - +
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Residues in contact with GLU 78 (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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6A PHE* 5.0 5.0 - - - +
7A TRP* 3.3 42.5 + - + +
43A PHE* 4.0 23.3 - - + -
74A SER 3.6 6.8 - - - +
75A ARG* 3.4 27.4 - - + +
77A ARG* 1.3 82.0 + - - +
79A CYS* 1.3 57.7 + - - +
82A TYR* 2.9 39.4 + - + +
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Residues in contact with CYS 79 (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 PHE* 4.4 15.0 - - - -
65A LEU* 4.0 19.3 - - - +
68A ILE* 4.6 8.5 - - - -
69A TYR* 4.1 26.2 - - + -
75A ARG* 2.8 30.9 + - - +
76A ARG 3.0 5.0 + - - +
78A GLU* 1.3 78.3 - - - +
80A LEU* 1.3 58.3 + - - +
82A TYR* 4.4 4.5 - - - -
83A LEU* 2.6 53.3 + - + +
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Residues in contact with LEU 80 (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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69A TYR* 4.5 17.9 - - + +
76A ARG* 2.7 40.0 + - + +
77A ARG* 3.9 7.9 - - + +
79A CYS* 1.3 72.4 - - - +
81A TYR* 1.3 55.4 + - - +
83A LEU* 3.5 6.6 + - + +
84A THR* 2.7 34.3 + - - -
99A TYR* 3.5 50.8 - - + +
100A VAL* 5.7 0.2 - - - -
102A THR* 4.7 20.6 - - + -
103A LEU* 4.4 19.3 - - + -
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Residues in contact with TYR 81 (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* 4.0 36.3 - + + +
8A PRO* 3.6 25.6 + - + -
9A THR* 4.8 4.0 - - - -
10A LEU 4.8 2.8 + - - -
77A ARG 3.0 17.9 + - - +
78A GLU 3.9 2.7 - - - +
80A LEU* 1.3 77.3 - - - +
82A TYR* 1.3 72.0 + + - +
84A THR* 3.2 15.6 + - - -
85A ILE* 3.2 35.3 + - + +
100A VAL* 5.9 1.3 - - + -
103A LEU* 3.9 23.2 - - + +
112A GLN* 3.9 21.5 + - + +
113A VAL* 4.2 20.2 - - + -
116A LEU* 3.4 33.0 - - + +
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Residues in contact with TYR 82 (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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6A PHE 5.4 1.4 + - - -
7A TRP* 4.5 13.0 - + - -
8A PRO* 3.9 24.6 - - + +
43A PHE* 3.3 37.8 - + - -
47A TRP* 3.2 51.9 - + + -
50A ILE* 4.4 3.6 - - + +
65A LEU* 3.7 28.7 - - + +
78A GLU* 2.9 30.9 + - + +
79A CYS 3.8 0.4 - - - +
81A TYR* 1.3 93.6 - + + +
83A LEU* 1.3 58.0 + - - +
85A ILE* 3.3 8.1 + - + +
86A GLY* 2.8 27.7 + - - -
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Residues in contact with LEU 83 (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 VAL* 4.0 11.2 - - + +
65A LEU* 3.5 35.9 - - + +
66A THR* 3.8 19.5 - - + +
69A TYR* 5.0 8.1 - - + -
79A CYS* 2.6 44.0 + - + +
80A LEU* 3.9 8.5 - - + +
82A TYR* 1.3 72.7 - - - +
84A THR* 1.3 54.0 + - - +
86A GLY* 4.4 0.7 - - - +
87A CYS* 2.6 48.9 + - - +
99A TYR* 4.2 36.8 - - + -
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Residues in contact with THR 84 (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 2.7 21.5 + - - -
81A TYR* 3.2 8.5 + - - -
83A LEU* 1.3 77.8 - - - +
85A ILE* 1.3 58.5 + - - +
87A CYS* 3.8 0.9 - - - +
88A TYR* 2.8 29.8 + - - +
96A ALA* 4.0 15.4 + - + +
99A TYR* 4.3 1.5 - - - +
100A VAL* 3.6 33.8 + - + +
103A LEU* 6.1 0.2 - - - +
116A LEU* 3.7 24.7 - - + -
120A VAL* 3.7 27.1 - - + -
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Residues in contact with ILE 85 (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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8A PRO* 6.1 0.7 - - + -
9A THR 4.8 4.0 - - - +
10A LEU* 3.5 39.9 - - + -
13A ALA* 4.6 8.7 - - + -
47A TRP* 4.7 20.4 - - + -
50A ILE* 4.5 14.8 - - + -
81A TYR* 3.2 41.0 + - + +
82A TYR* 3.7 9.0 - - + +
83A LEU 3.2 0.4 - - - -
84A THR* 1.3 75.0 - - - +
86A GLY* 1.3 66.7 + - - +
87A CYS 3.2 0.5 + - - -
88A TYR* 3.2 15.0 + - - +
89A LYS* 3.4 16.4 + - - +
116A LEU* 3.8 17.0 - - + -
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Residues in contact with GLY 86 (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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50A ILE* 4.0 29.1 - - - +
58A GLU* 4.8 3.7 - - - +
62A VAL* 3.9 14.3 - - - +
65A LEU* 5.5 0.2 - - - -
82A TYR 2.8 19.6 + - - -
83A LEU 3.9 0.4 - - - -
85A ILE* 1.3 74.6 - - - +
87A CYS* 1.3 60.1 + - - +
89A LYS* 3.7 8.1 + - - +
90A LEU* 3.6 20.6 - - - +
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Residues in contact with CYS 87 (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 VAL* 4.2 19.5 - - - -
83A LEU* 2.6 44.3 + - - +
86A GLY* 1.3 71.3 - - - +
88A TYR* 1.3 60.6 + - - +
89A LYS 3.1 2.0 - - - -
90A LEU* 2.7 27.0 + - - -
91A GLY 3.1 7.4 + - - -
92A GLU* 3.4 15.0 + - + +
95A MET* 4.3 18.8 - - - -
96A ALA* 3.7 24.2 - - + +
99A TYR* 4.9 3.4 - - - -
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Residues in contact with TYR 88 (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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10A LEU* 4.8 20.9 - - + -
14A TYR* 5.2 11.0 + + - -
84A THR* 2.8 19.4 + - + +
85A ILE* 3.2 8.5 + - - +
87A CYS* 1.3 76.5 - - - +
89A LYS* 1.3 73.6 + - + +
91A GLY* 3.0 13.8 + - - +
93A TYR* 3.8 34.1 + + - -
96A ALA* 4.5 2.2 - - - +
116A LEU* 5.7 2.9 - - + -
119A MET* 3.8 41.8 - - + +
120A VAL* 4.8 8.3 - - + -
123A LYS* 4.4 16.7 + - + +
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Residues in contact with LYS 89 (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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10A LEU* 5.6 1.6 - - - -
13A ALA* 3.7 41.7 + - - +
14A TYR* 6.0 3.1 - - - -
50A ILE* 2.6 33.3 + - + +
51A LYS* 3.9 1.8 - - - +
52A SER 4.2 4.9 + - - -
55A VAL* 5.1 3.3 - - - +
58A GLU* 3.7 30.5 - - + +
85A ILE* 3.4 12.5 + - - +
86A GLY 3.9 8.1 - - - +
87A CYS 3.1 0.8 + - - -
88A TYR* 1.3 89.3 - - + +
90A LEU* 1.3 62.6 + - - +
91A GLY 3.2 1.1 + - - -
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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