Contacts of the helix formed by residues 87 - 105 (chain B) in PDB entry 2YXU
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LEU 5.6 0.2 - - - +
58B ASN* 5.7 1.6 - - - +
59B SER* 4.9 1.9 + - - -
85B THR* 3.6 3.1 + - - +
86B ARG* 1.3 111.5 + - - +
88B LYS* 1.3 58.7 + - - +
89B SER* 3.3 23.7 + - - -
90B PHE* 2.9 51.6 + - - +
91B LEU* 3.0 12.4 + - - +
129B PRO* 4.9 2.7 - - + -
132B LEU* 3.6 6.7 - - - -
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 1.3 73.5 + - - +
89B SER* 1.3 57.2 + - - +
91B LEU* 3.7 3.3 - - - +
92B ALA* 2.9 33.3 + - + +
129B PRO* 5.7 0.4 - - - +
131B ASP* 3.2 38.3 + - - +
132B LEU* 3.1 22.7 - - + +
135B VAL* 4.0 28.8 - - + +
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 2.7 32.4 + - - -
87B ASP* 3.2 17.1 + - - -
88B LYS* 1.3 79.6 - - - +
90B PHE* 1.3 62.9 + - - +
92B ALA* 3.6 6.0 + - - +
93B MET* 3.2 15.6 + - - +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.8 25.4 - - + -
40B SER* 3.6 29.6 - - - -
57B LEU* 3.3 40.4 - - + -
58B ASN* 4.2 0.4 - - - -
59B SER* 3.9 19.3 + - - -
62B LEU* 3.9 26.2 - - + -
85B THR* 3.8 20.4 - - + -
86B ARG* 5.9 4.3 - - + +
87B ASP* 2.9 26.8 + - - +
89B SER* 1.3 75.6 - - - +
91B LEU* 1.3 54.8 + - - +
93B MET* 3.0 5.9 + - - +
94B VAL* 2.8 44.9 + - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B THR* 5.9 2.5 - - - +
85B THR* 3.9 23.1 - - + +
87B ASP 3.0 9.0 + - - +
88B LYS* 3.4 9.6 + - - +
90B PHE* 1.3 76.3 - - - +
92B ALA* 1.3 59.3 + - - +
94B VAL* 3.1 13.8 + - + +
95B VAL* 2.8 34.5 + - + +
110B TYR* 5.6 0.9 - - - +
132B LEU* 3.8 18.6 - - + -
135B VAL* 3.9 18.2 - - + -
136B TYR* 3.7 38.8 - - + +
140B VAL* 3.7 26.5 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LYS* 2.9 20.2 + - + +
89B SER* 3.8 6.7 - - - +
91B LEU* 1.3 76.0 - - - +
93B MET* 1.3 62.7 + - - +
95B VAL* 3.4 10.1 + - - +
96B ASP* 3.1 28.8 + - - +
135B VAL* 4.7 10.0 - - + +
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Residues in contact with MET 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 3.6 23.6 - - - +
62B LEU* 3.5 23.1 - - + -
63B GLN* 3.4 48.5 - - + +
89B SER 3.2 11.9 + - - +
90B PHE 3.0 12.7 + - - +
92B ALA* 1.3 78.2 - - - +
94B VAL* 1.3 63.2 + - - +
96B ASP* 3.1 18.7 + - - +
97B ILE* 3.0 32.6 + - - +
1527B PO4 4.4 7.0 - - - +
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 4.3 17.0 - - + -
62B LEU* 4.0 9.9 - - + -
82B THR* 3.5 30.7 - - + -
85B THR* 5.2 3.4 - - + +
90B PHE* 2.8 47.1 + - + +
91B LEU* 3.1 18.5 + - + +
93B MET* 1.3 72.3 - - - +
95B VAL* 1.3 59.0 + - + +
97B ILE* 3.3 7.8 + - - +
98B VAL* 2.9 38.0 + - + +
110B TYR* 4.6 5.4 - - - +
140B VAL* 6.4 0.2 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 2.8 19.6 + - + +
92B ALA* 3.5 11.7 - - - +
94B VAL* 1.3 77.7 - - + +
96B ASP* 1.3 62.2 + - - +
98B VAL* 3.3 2.1 + - - -
99B GLN* 2.8 44.0 + - - +
110B TYR* 6.4 1.1 - - + -
135B VAL* 4.9 0.9 - - + -
139B LYS* 4.1 32.1 - - + +
140B VAL* 3.4 32.3 - - + -
143B LEU* 3.7 21.4 - - + +
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 3.1 21.9 + - - +
93B MET* 3.1 19.2 + - - +
95B VAL* 1.3 77.4 - - - +
97B ILE* 1.3 63.5 + - - +
99B GLN* 3.4 17.4 + - - +
100B GLU* 3.2 22.2 + - - +
1527B PO4 3.8 24.6 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.5 11.0 - - + -
10B ILE* 5.0 8.3 - - + -
62B LEU* 3.5 44.2 - - + +
66B TYR* 4.0 41.3 - - + -
80B VAL* 6.3 0.2 - - + -
93B MET* 3.0 26.1 + - + +
94B VAL* 3.6 7.6 - - - +
96B ASP* 1.3 74.1 - - - +
98B VAL* 1.3 68.0 + - + +
99B GLN 3.2 0.2 + - - -
100B GLU* 3.2 5.5 + - - +
101B LEU* 3.0 40.9 + - + +
1527B PO4 4.4 6.5 - - - +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 6.0 0.4 - - + -
80B VAL* 3.9 28.5 - - + -
94B VAL* 2.9 28.6 + - + +
95B VAL* 3.8 4.5 - - - +
97B ILE* 1.3 78.2 - - + +
99B GLN* 1.3 63.1 + - - +
101B LEU* 3.4 7.1 + - - +
102B LYS* 2.9 31.8 + - + +
108B LEU* 4.9 3.8 - - + -
110B TYR* 3.9 30.3 - - + -
143B LEU* 3.6 25.8 - - + -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B VAL* 2.8 35.9 + - - +
96B ASP* 3.4 17.4 + - - +
97B ILE 3.2 0.2 - - - -
98B VAL* 1.3 76.9 - - - +
100B GLU* 1.3 62.3 + - - +
102B LYS* 3.2 8.1 + - - +
103B GLN* 3.1 33.0 + - - +
139B LYS* 5.7 5.5 - - - +
143B LEU* 3.8 26.8 - - + +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TYR* 2.8 33.0 + - + +
70B ARG* 3.8 13.2 + - - -
75B ASN* 3.6 10.4 + - - -
96B ASP 3.2 12.6 + - - +
97B ILE* 3.9 2.2 - - - +
99B GLN* 1.3 78.8 - - - +
101B LEU* 1.3 64.3 + - - +
103B GLN* 3.3 17.5 + - + +
104B GLN* 3.0 32.5 + - + +
1527B PO4 2.7 28.8 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.9 22.9 - - + -
66B TYR* 3.5 23.1 - - + +
75B ASN* 3.4 34.1 - - + +
76B LYS* 5.1 1.1 - - - -
77B TYR* 4.1 13.5 + - + +
80B VAL* 3.7 24.5 - - + -
97B ILE* 3.0 28.4 + - + +
98B VAL* 3.9 4.5 - - - +
100B GLU* 1.3 77.0 - - - +
102B LYS* 1.3 58.3 + - - +
104B GLN* 3.3 4.5 + - - +
105B ASN* 2.9 26.5 + - - +
108B LEU* 3.6 20.7 - - + +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 2.9 20.4 + - + +
99B GLN* 3.6 5.2 - - - +
100B GLU 3.2 0.2 - - - -
101B LEU* 1.3 75.2 - - - +
103B GLN* 1.3 63.7 + - - +
105B ASN 3.7 5.2 - - - +
106B PRO* 3.0 32.3 - - + +
108B LEU* 3.5 34.8 - - + +
110B TYR* 4.1 4.0 - - - -
143B LEU* 2.7 48.1 + - + +
145B ASP* 2.9 32.1 + - - -
1015B MPD 4.0 8.9 - - - +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLN* 3.1 26.4 + - - +
100B GLU* 3.3 18.3 + - + +
102B LYS* 1.3 76.5 - - - +
104B GLN* 1.3 64.2 + - + +
105B ASN* 3.4 0.5 + - - -
106B PRO* 4.5 7.7 - - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASN* 5.5 2.2 - - - +
75B ASN* 3.5 46.3 + - - +
76B LYS* 3.6 28.7 + - + +
100B GLU* 3.0 27.6 + - + +
101B LEU* 3.4 9.0 - - - +
103B GLN* 1.3 78.3 - - - +
105B ASN* 1.3 62.2 + - + +
106B PRO* 4.2 2.1 - - - +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 5.5 4.9 - - + -
77B TYR 2.8 33.7 + - - +
78B ASP* 4.1 11.5 + - - +
101B LEU 2.9 10.5 + - - +
102B LYS* 3.0 7.5 - - - +
103B GLN 3.2 0.6 - - - -
104B GLN* 1.3 82.1 - - + +
106B PRO* 1.3 63.6 - - - +
107B ARG* 2.8 43.7 + - - +
108B LEU* 2.9 30.6 + - - +
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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