Contacts of the helix formed by residues 98 - 110 (chain B) in PDB entry 5SZK
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ASP* 2.9 35.2 + - - +
94B GLU* 2.9 46.2 + - - +
95B SER 3.9 2.9 - - - +
96B TYR 3.2 0.2 - - - -
97B ALA* 1.3 74.5 - - - +
99B VAL* 1.3 65.2 + - - +
100B LYS 3.1 0.7 - - - -
101B GLN* 2.6 45.1 + - + +
102B TRP* 3.0 18.3 + - - +
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Residues in contact with VAL 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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86B VAL* 4.2 13.9 - - + +
87B VAL 5.2 0.9 - - - +
88B TYR* 3.9 17.9 - - + -
95B SER 3.5 11.9 + - - +
96B TYR* 3.2 21.3 - - + +
97B ALA 3.0 0.8 + - - -
98B ASN* 1.3 77.1 - - - +
100B LYS* 1.3 63.3 + - - +
102B TRP* 3.0 11.5 + - + +
103B LEU* 2.9 30.5 + - + +
118B LEU* 3.8 33.0 - - + -
139B PHE* 3.8 25.4 - - + -
145B ILE* 6.4 0.2 - - + -
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Residues in contact with LYS 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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96B TYR* 4.8 13.1 + - - +
97B ALA* 3.4 28.2 + - - +
98B ASN 3.1 0.6 - - - -
99B VAL* 1.3 78.2 - - + +
101B GLN* 1.3 70.0 + - - +
103B LEU* 3.2 13.0 + - - +
104B GLN* 3.0 28.2 + - + +
139B PHE* 4.0 33.5 - - + -
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Residues in contact with GLN 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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71B ARG* 4.4 14.3 + - - +
97B ALA 4.4 3.8 - - - +
98B ASN* 2.6 41.1 + - + +
100B LYS* 1.3 87.3 - - - +
102B TRP* 1.3 58.2 + - + +
104B GLN* 3.2 18.6 + - - +
105B GLU* 2.9 30.6 + - - +
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Residues in contact with TRP 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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14B ILE* 3.9 11.8 - - + +
15B GLY* 3.4 41.5 - - - -
16B ASP* 2.9 35.7 + - - +
64B THR* 6.1 0.2 - - - -
65B ALA 5.1 2.5 - - - -
66B GLY* 4.0 19.7 - - - -
71B ARG* 3.7 42.8 - - + -
74B THR* 5.9 1.3 - - - -
78B TYR* 3.8 24.7 - - - -
86B VAL* 3.9 16.4 - - + -
87B VAL 5.3 1.1 - - - -
95B SER 5.4 1.6 - - - -
98B ASN* 3.0 27.3 + - + +
99B VAL* 3.0 11.0 + - + +
101B GLN* 1.3 73.2 - - + +
103B LEU* 1.3 60.8 + - - +
105B GLU* 3.2 7.1 + - + +
106B ILE* 3.0 33.0 + - - +
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Residues in contact with LEU 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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86B VAL* 4.3 10.1 - - + -
99B VAL* 2.9 34.2 + - + +
100B LYS* 3.2 11.0 + - - +
102B TRP* 1.3 76.8 - - - +
104B GLN* 1.3 58.0 + - + +
106B ILE* 3.1 14.6 + - + +
107B ASP* 3.0 35.0 + - - +
116B LYS* 3.8 30.7 - - + -
139B PHE* 4.0 23.1 - - + -
143B LEU* 4.9 12.6 - - + -
145B ILE* 4.9 15.3 - - + -
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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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100B LYS* 3.0 17.4 + - - +
101B GLN* 3.2 20.3 + - - +
103B LEU* 1.3 75.0 - - + +
105B GLU* 1.3 61.0 + - - +
107B ASP* 3.4 10.3 + - - +
108B ARG* 3.0 29.5 + - - +
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Residues in contact with GLU 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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71B ARG* 3.6 46.5 + - - +
75B SER* 4.4 5.9 - - - -
78B TYR* 3.7 27.6 + - + +
101B GLN 2.9 11.8 + - - +
102B TRP* 3.4 15.3 - - + +
104B GLN* 1.3 74.3 - - - +
106B ILE* 1.3 64.2 + - - +
108B ARG* 3.4 7.7 + - - -
109B TYR* 3.1 59.0 + - - +
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Residues in contact with ILE 106 (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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14B ILE* 3.9 13.0 - - + -
78B TYR* 4.1 6.7 - - + -
84B ILE* 3.9 25.8 - - + -
86B VAL* 3.6 31.2 - - + -
102B TRP 3.0 16.3 + - - +
103B LEU* 3.4 11.2 - - + +
105B GLU* 1.3 76.0 - - - +
107B ASP* 1.3 64.8 + - - +
108B ARG 3.0 0.2 + - - -
110B ALA* 2.8 47.8 + - + +
111B SER 5.6 1.1 - - - +
114B VAL* 5.0 4.3 - - + -
116B LYS* 4.0 37.7 - - + +
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Residues in contact with ASP 107 (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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103B LEU* 3.0 21.7 + - - +
104B GLN* 4.0 9.2 - - - +
105B GLU 3.4 0.2 - - - -
106B ILE* 1.3 77.3 - - - +
108B ARG* 1.3 59.4 + - - +
110B ALA 4.7 4.5 - - - +
116B LYS* 3.5 24.7 + - - -
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Residues in contact with ARG 108 (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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79B ARG* 5.7 1.4 + - - -
104B GLN 3.0 17.6 + - - +
105B GLU* 3.8 8.7 + - - +
106B ILE 3.1 0.4 - - - -
107B ASP* 1.3 79.6 - - - +
109B TYR* 1.3 111.2 + - + +
110B ALA 4.9 1.4 - - - +
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Residues in contact with TYR 109 (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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75B SER* 3.7 38.9 + - - +
78B TYR* 3.8 16.6 - + + -
79B ARG* 3.5 29.9 + - - +
105B GLU* 3.1 39.0 + - - +
108B ARG* 1.3 135.3 + - + +
110B ALA* 1.3 66.8 + - - +
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Residues in contact with ALA 110 (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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78B TYR* 3.9 13.1 - - + +
79B ARG* 2.6 25.0 + - - -
84B ILE* 3.8 15.0 - - + -
106B ILE* 2.8 40.7 + - + +
107B ASP 4.7 4.3 - - - +
108B ARG 4.9 0.7 - - - -
109B TYR* 1.3 75.4 + - - +
111B SER* 1.3 59.5 + - - +
112B GLU* 4.9 0.2 - - - -
114B VAL* 3.5 17.7 - - + -
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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