Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 2YB6
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 ASP 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.8 5.2 - - - +
12A ASP* 3.4 23.7 - - - +
15A ARG* 4.2 27.0 + - - +
63A TYR* 3.5 8.7 - - - -
99A THR 4.0 3.3 + - - +
100A TYR* 1.3 75.7 - - - +
102A VAL* 1.3 67.5 + - - +
103A SER* 3.3 15.7 + - - -
104A SER* 3.0 23.9 + - - -
105A ILE* 2.9 27.1 + - - +
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Residues in contact with VAL 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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9A LEU* 4.7 0.2 - - + -
12A ASP* 3.0 26.2 + - + +
16A LEU* 4.0 7.0 - - + -
36A TRP* 3.7 38.6 - - + -
57A ILE* 3.8 15.5 - - + -
59A PHE* 3.4 31.2 - - + -
63A TYR* 3.9 0.2 + - - -
101A ASP* 1.3 76.1 - - - +
103A SER* 1.3 64.2 + - - +
105A ILE* 3.3 8.0 + - - +
106A LEU* 2.9 43.0 + - + +
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Residues in contact with SER 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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12A ASP 4.6 1.5 + - - -
15A ARG* 4.4 2.3 - - - +
16A LEU* 3.3 46.4 + - - +
19A ASP 5.2 1.5 + - - -
21A PRO* 4.3 13.2 - - - +
101A ASP* 3.2 15.2 + - - -
102A VAL* 1.3 80.2 - - - +
104A SER* 1.3 58.4 + - - +
106A LEU* 3.9 3.6 - - - +
107A THR* 2.9 31.8 + - - -
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Residues in contact with SER 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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91A ILE* 5.0 2.7 - - - -
99A THR 4.7 0.9 + - - -
100A TYR* 3.5 21.6 - - - -
101A ASP* 3.0 31.1 + - - -
103A SER* 1.3 76.7 - - - +
105A ILE* 1.3 59.5 + - - +
107A THR* 3.7 7.1 - - - -
108A SER* 2.8 34.2 + - - -
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Residues in contact with ILE 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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57A ILE* 5.7 4.3 - - + -
59A PHE* 5.2 1.6 - - + -
63A TYR* 4.8 3.4 - - - +
68A PRO* 3.7 26.5 - - + -
70A VAL* 4.1 16.4 - - + -
89A LEU* 4.4 1.7 - - + +
91A ILE* 4.4 9.4 - - + -
92A LEU* 4.2 13.5 - - + -
96A TRP* 3.9 28.9 - - + -
100A TYR* 4.6 2.7 - - + -
101A ASP* 2.9 26.2 + - - +
102A VAL* 3.6 9.4 - - + +
104A SER* 1.3 76.2 + - - +
106A LEU* 1.3 61.9 + - + +
108A SER* 3.2 6.9 + - - -
109A ILE* 3.0 46.0 + - + +
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Residues in contact with LEU 106 (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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16A LEU* 4.2 6.5 - - + -
24A VAL* 4.1 17.6 - - + +
25A SER 3.7 32.5 - - - +
26A GLY* 4.5 0.7 - - - +
38A ALA* 3.8 22.0 - - + -
40A ILE* 3.5 25.9 - - + +
55A LEU* 4.6 5.6 - - + -
57A ILE* 4.1 12.3 - - + -
102A VAL* 2.9 37.4 + - + +
103A SER 3.9 3.4 - - - +
105A ILE* 1.3 80.0 - - + +
107A THR* 1.3 56.4 + - - +
109A ILE* 3.3 12.1 + - + -
110A GLN* 2.9 26.7 + - - +
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Residues in contact with THR 107 (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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21A PRO* 3.5 27.7 - - + +
24A VAL* 4.4 8.0 - - - +
103A SER 2.9 18.3 + - - -
104A SER* 3.7 9.3 - - - -
106A LEU* 1.3 76.2 - - - +
108A SER* 1.3 58.5 + - - +
110A GLN* 3.2 9.1 + - - +
111A SER* 2.9 37.7 + - - +
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Residues in contact with SER 108 (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 LEU* 3.9 24.4 - - - +
91A ILE* 3.7 15.6 - - - +
100A TYR* 5.3 2.8 - - - -
104A SER* 2.8 22.6 + - - -
105A ILE 3.4 5.2 - - - -
107A THR* 1.3 78.8 - - - +
109A ILE* 1.3 57.3 + - - +
111A SER* 3.3 7.4 + - - -
112A LEU* 2.8 29.0 + - - +
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Residues in contact with ILE 109 (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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40A ILE* 3.6 15.7 - - + -
55A LEU* 4.2 4.3 - - + -
70A VAL* 3.7 34.1 - - + -
72A PHE* 3.8 25.4 - - + -
87A ILE* 4.1 22.0 - - + -
89A LEU* 3.9 15.5 - - + -
92A LEU* 5.0 0.4 - - + -
105A ILE* 3.0 33.7 + - + +
106A LEU* 3.3 10.7 + - + +
108A SER* 1.3 73.1 - - - +
110A GLN* 1.3 65.7 + - - +
112A LEU* 3.2 17.8 + - + +
113A LEU* 3.2 14.4 + - + +
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Residues in contact with GLN 110 (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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22A VAL* 3.2 30.0 + - - +
23A GLY* 3.8 12.5 + - - -
24A VAL* 4.1 5.8 - - + +
40A ILE* 3.7 16.5 - - + +
41A PHE* 3.0 28.6 + - - +
42A GLY 4.8 0.2 + - - -
43A PRO* 3.8 30.6 - - + +
106A LEU 2.9 13.7 + - - +
107A THR* 3.2 12.6 + - - +
109A ILE* 1.3 76.4 - - - +
111A SER* 1.3 66.0 + - - +
113A LEU* 3.2 21.1 + - - +
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 5.5 2.7 - - - -
107A THR* 2.9 23.9 + - - +
108A SER* 3.7 7.2 - - - -
110A GLN* 1.3 78.0 + - - +
112A LEU* 1.3 65.9 + - - +
114A ASP* 3.1 15.0 + - - +
115A GLU* 3.2 19.5 + - - +
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Residues in contact with LEU 112 (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 PHE* 6.2 0.4 - - + -
78A HIS* 2.8 22.8 + - + +
80A ASN* 3.4 31.4 - - + +
81A VAL* 5.3 3.6 - - + -
87A ILE* 3.9 20.2 - - + -
88A CYS 3.6 19.5 - - - +
89A LEU* 4.0 18.4 - - + -
108A SER 2.8 18.5 + - - +
109A ILE* 3.3 15.5 - - + +
111A SER* 1.3 72.0 - - - +
113A LEU* 1.3 65.9 + - + +
115A GLU* 2.9 29.4 + - - +
117A ASN 4.4 0.9 - - - +
1153A CL 4.4 13.2 - - + -
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Residues in contact with LEU 113 (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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40A ILE* 4.5 6.7 - - + -
42A GLY* 4.4 2.0 - - - -
43A PRO* 4.0 21.1 - - + -
48A PHE* 3.1 45.7 - - + -
53A PHE* 4.2 28.0 - - + -
72A PHE* 4.1 24.9 - - + -
76A MET* 4.1 7.9 - - - -
78A HIS* 3.3 26.0 + - + -
81A VAL* 5.7 0.4 - - + -
109A ILE* 3.2 13.2 + - + +
110A GLN* 3.2 14.3 + - - +
111A SER 3.1 1.4 - - - -
112A LEU* 1.3 80.3 - - + +
114A ASP* 1.3 58.2 + - - +
116A PRO* 4.5 1.9 - - - +
137A TYR* 4.4 2.6 + - - -
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Residues in contact with ASP 114 (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 PRO* 4.3 6.7 - - + -
46A THR* 3.3 41.8 - - + +
47A PRO* 3.9 11.1 - - - +
48A PHE* 5.2 0.7 - - - -
110A GLN 4.1 0.6 + - - -
111A SER* 3.1 8.8 + - - +
113A LEU* 1.3 76.0 - - - +
115A GLU* 1.3 74.2 + - + +
116A PRO* 3.6 9.1 - - - +
130A TYR* 4.4 6.2 + - - -
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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