Contacts of the helix formed by residues 100 - 116 (chain B) in PDB entry 5LSJ
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 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 3.9 7.4 + - - -
97B GLU* 4.2 7.3 + - - +
98B GLU 3.6 2.2 - - - -
99B GLY* 1.3 80.8 - - - +
101B LEU* 1.3 59.3 + - - +
102B GLU* 3.2 4.3 - - - +
103B ALA* 2.9 19.4 + - + +
104B VAL* 2.8 28.8 + - + +
140E TYR* 5.4 6.5 - - - -
143E GLN* 3.6 23.9 + - - +
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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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13A PHE* 5.8 0.7 - - + -
15A PHE* 4.5 26.7 - - + -
20A CYS* 5.2 8.5 - - - -
91A LEU* 5.4 6.5 - - + -
38B LEU* 6.2 2.5 - - + -
95B ILE* 3.8 24.9 - - + +
96B LYS* 3.1 13.7 + - + +
98B GLU* 3.5 25.8 - - - +
99B GLY* 3.2 21.0 - - - +
100B ASN* 1.3 74.5 - - - +
102B GLU* 1.3 60.8 + - - +
104B VAL* 3.6 13.0 - - + -
105B LEU* 2.9 51.1 + - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 4.3 20.1 - - + +
96B LYS* 3.2 54.0 + - + +
97B GLU* 5.2 6.8 - - - +
100B ASN* 3.2 0.6 - - - -
101B LEU* 1.3 78.5 - - - +
103B ALA* 1.3 57.1 + - - +
105B LEU* 3.9 0.3 - - - +
106B ASN* 2.9 40.6 + - - +
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Residues in contact with ALA 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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100B ASN* 2.9 25.3 + - + +
102B GLU* 1.3 79.6 - - - +
104B VAL* 1.3 59.1 + - + +
106B ASN* 3.4 6.9 + - - +
107B ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 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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12A PHE* 3.7 14.9 - - + +
13A PHE* 4.4 21.5 - - + -
15A PHE* 5.9 1.1 - - + -
99B GLY 4.0 11.0 - - - +
100B ASN* 2.8 21.0 + - + +
101B LEU* 3.6 30.3 - - + +
103B ALA* 1.3 73.7 - - + +
105B LEU* 1.3 65.8 + - - +
107B ALA* 3.4 7.6 + - - +
108B LEU* 2.9 26.3 + - - +
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Residues in contact with LEU 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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13A PHE* 3.5 34.3 - - + -
90A ILE* 3.7 32.8 - - + -
91A LEU* 4.5 3.6 - - + -
34B ARG* 3.9 22.2 - - + +
35B VAL* 4.6 13.7 - - + -
38B LEU* 4.4 18.4 - - + -
96B LYS* 6.4 1.3 - - + -
101B LEU* 2.9 37.2 + - + +
102B GLU 4.2 1.3 - - - +
104B VAL* 1.3 75.0 - - + +
106B ASN* 1.3 60.6 + - - +
108B LEU* 3.4 4.8 + - + +
109B ASP* 2.7 32.9 + - - +
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Residues in contact with ASN 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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33B SER* 3.5 14.7 - - - +
35B VAL* 3.9 13.2 - - - +
102B GLU* 2.9 29.7 + - - +
103B ALA* 3.7 6.8 - - - +
105B LEU* 1.3 76.1 - - - +
107B ALA* 1.3 60.0 + - - +
109B ASP* 3.0 17.8 + - - +
110B LYS* 2.9 26.0 + - - +
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Residues in contact with ALA 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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12A PHE* 4.9 7.0 - - + -
103B ALA 2.9 17.6 + - - +
104B VAL* 3.7 9.0 - - - +
105B LEU 3.3 0.2 - - - -
106B ASN* 1.3 75.5 - - - +
108B LEU* 1.3 57.2 + - - +
110B LYS* 3.3 10.9 + - + +
111B ILE* 2.9 39.4 + - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.5 27.3 - - + -
13A PHE* 3.7 29.2 - - + -
91A LEU 4.8 0.2 - - - +
92A ARG 4.0 10.8 - - - +
93A ILE* 4.1 15.9 - - + -
94A PRO* 5.0 2.9 - - + -
97A ILE* 5.5 0.4 - - + -
99A LEU* 5.6 0.7 - - + -
34B ARG* 3.4 36.6 - - - +
104B VAL 2.9 13.1 + - - +
105B LEU* 3.5 6.7 - - + +
107B ALA* 1.3 75.0 - - - +
109B ASP* 1.3 59.0 + - - +
111B ILE* 4.3 11.9 - - + -
112B VAL* 2.8 48.1 + - + +
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Residues in contact with ASP 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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31B THR* 4.8 5.8 - - - +
33B SER* 2.8 39.1 + - - +
34B ARG* 3.2 33.0 + - - +
105B LEU 2.7 22.5 + - - +
106B ASN* 3.0 16.0 + - - +
108B LEU* 1.3 76.1 - - - +
110B LYS* 1.3 57.2 + - - +
112B VAL* 3.2 4.4 + - - +
113B GLU* 2.9 33.2 + - + +
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Residues in contact with LYS 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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106B ASN 2.9 11.1 + - - +
107B ALA* 3.5 13.2 - - + +
109B ASP* 1.3 76.4 - - - +
111B ILE* 1.3 61.6 + - + +
113B GLU* 3.0 6.3 + - - +
114B GLU* 2.9 59.9 + - + +
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Residues in contact with ILE 111 (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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12A PHE* 4.2 24.7 - - + -
97A ILE* 3.5 29.3 - - + +
98A LEU 4.4 4.3 - - - +
99A LEU* 4.6 6.7 - - + -
100A PRO* 3.7 40.4 - - + -
107B ALA* 2.9 24.8 + - + +
108B LEU* 3.8 9.0 - - + +
110B LYS* 1.3 77.9 - - + +
112B VAL* 1.3 58.5 + - - +
114B GLU* 4.1 9.7 - - - +
115B GLY* 3.0 21.3 + - - -
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Residues in contact with VAL 112 (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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94A PRO* 3.8 26.0 - - + -
97A ILE* 3.6 15.6 - - + +
34B ARG* 3.7 23.3 - - - +
108B LEU* 2.8 32.8 + - + +
109B ASP* 3.6 4.3 - - - +
110B LYS 3.1 0.2 - - - -
111B ILE* 1.3 76.7 - - - +
113B GLU* 1.3 69.2 + - + +
116B LYS* 3.1 45.6 + - + +
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Residues in contact with GLU 113 (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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31B THR* 4.0 27.2 - - + +
109B ASP* 2.9 18.0 + - + +
110B LYS* 3.0 8.9 + - - +
112B VAL* 1.3 83.6 - - + +
114B GLU* 1.3 63.7 + - + +
116B LYS* 3.3 27.0 + - - +
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Residues in contact with GLU 114 (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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110B LYS* 2.9 47.3 + - + +
111B ILE* 4.3 8.8 - - - +
113B GLU* 1.3 77.5 - - + +
115B GLY* 1.3 62.4 + - - +
116B LYS 3.5 6.9 + - - +
117B VAL* 5.0 3.1 - - - +
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Residues in contact with GLY 115 (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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96A ASN* 4.4 6.2 - - - +
97A ILE* 4.1 16.3 - - - +
98A LEU 5.7 2.5 - - - -
111B ILE 3.0 20.1 + - - -
112B VAL 4.0 0.9 - - - -
113B GLU 3.2 0.2 - - - -
114B GLU* 1.3 74.6 - - - +
116B LYS* 1.3 64.3 + - - +
117B VAL* 3.5 2.6 + - - +
118B ARG* 3.6 19.8 + - - +
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Residues in contact with LYS 116 (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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94A PRO* 4.8 6.9 - - - +
96A ASN* 3.1 31.7 - - - +
97A ILE* 4.3 3.9 - - + +
112B VAL* 3.1 37.5 + - + +
113B GLU* 3.6 21.4 - - - +
114B GLU 3.3 7.2 - - - +
115B GLY* 1.3 79.5 - - - +
117B VAL* 1.3 69.5 + - - +
119B LYS* 3.4 21.6 - - - +
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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