Contacts of the helix formed by residues 98 - 108 (chain B) in PDB entry 4J15
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 SER 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLU 5.1 0.2 - - - -
23B ASP* 2.9 27.1 + - - -
24B TYR* 3.7 26.9 - - - -
25B ALA* 3.3 12.1 - - - +
93B VAL* 4.1 4.3 - - - -
97B ALA* 1.3 75.6 - - - +
99B LYS* 1.3 64.6 + - - +
100B GLN* 3.2 11.9 + - - +
101B MET* 3.2 16.2 + - - +
102B VAL* 3.1 22.3 + - - +
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Residues in contact with LYS 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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22B GLU* 5.5 8.1 + - - +
24B TYR* 5.4 0.4 - - - -
74B LYS* 6.1 4.5 - - + -
93B VAL* 3.8 25.9 - - + +
98B SER* 1.3 75.0 - - - +
100B GLN* 1.3 73.5 + - - +
102B VAL* 3.5 3.9 + - - +
103B LYS* 3.1 23.9 + - - +
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Residues in contact with GLN 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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22B GLU* 3.8 28.1 + - - +
23B ASP* 3.1 38.9 - - + +
29B TYR* 3.6 7.4 + - - +
98B SER* 3.0 15.1 + - - +
99B LYS* 1.3 92.0 + - - +
101B MET* 1.3 55.8 + - - +
103B LYS* 3.3 8.7 + - + +
104B PHE* 3.0 28.1 + - - +
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Residues in contact with MET 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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25B ALA* 4.1 1.3 - - - -
28B ARG* 3.9 11.9 - - - +
29B TYR* 3.5 44.3 - - + -
91B VAL* 4.2 5.8 - - + -
97B ALA* 3.4 29.8 - - + -
98B SER* 3.2 16.5 + - - +
100B GLN* 1.3 75.7 - - - +
102B VAL* 1.3 64.6 + - - +
104B PHE* 3.2 3.1 + - - +
105B ALA* 2.9 23.4 + - - +
139B VAL* 4.0 14.6 - - + -
140B GLN* 3.3 33.2 - - - +
141B LYS* 3.8 11.0 - - - +
142B ILE* 4.1 10.1 - - + +
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Residues in contact with VAL 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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71B ALA* 5.6 1.1 - - + -
73B GLY 4.8 5.8 - - - +
74B LYS* 3.8 8.3 - - - +
75B GLN 3.8 32.1 - - - +
76B CYS* 3.9 5.5 - - + +
91B VAL* 4.0 11.9 - - + +
92B ALA 3.9 13.5 - - - +
93B VAL* 3.7 29.2 - - + +
97B ALA* 4.5 0.7 - - + -
98B SER 3.1 16.4 + - - +
99B LYS* 3.8 6.3 - - - +
100B GLN 3.4 0.2 - - - -
101B MET* 1.3 75.0 - - - +
103B LYS* 1.3 57.4 - - - +
105B ALA* 3.5 3.1 + - - +
106B ALA* 3.0 29.1 + - + +
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Residues in contact with LYS 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 LYS 3.1 18.1 + - - +
100B GLN* 3.6 8.5 - - + +
101B MET 3.2 0.2 - - - -
102B VAL* 1.3 77.9 - - - +
104B PHE* 1.3 61.8 + - - +
106B ALA* 3.3 8.0 + - + +
107B ASN* 2.9 44.7 + - - +
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Residues in contact with PHE 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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29B TYR* 3.6 30.5 - + + -
30B GLY* 3.6 37.9 - - - -
31B ILE* 4.0 23.1 - - + -
100B GLN 3.0 13.2 + - - +
101B MET 3.4 7.6 - - - +
103B LYS* 1.3 72.9 - - - +
105B ALA* 1.3 69.5 + - - +
107B ASN* 2.9 18.8 + - + +
108B ILE* 3.2 30.5 + - + +
142B ILE* 4.0 11.4 - - + -
144B VAL* 4.1 12.3 - - + -
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Residues in contact with ALA 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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69B SER* 4.7 1.4 + - - -
76B CYS* 3.9 8.0 - - - -
78B LEU* 3.9 12.9 - - + +
91B VAL* 3.8 28.7 - - + -
101B MET 2.9 19.1 + - - +
102B VAL 3.7 4.5 - - - +
104B PHE* 1.3 73.9 - - - +
106B ALA* 1.3 62.6 + - - +
107B ASN 3.1 1.4 + - - -
108B ILE* 3.2 32.7 + - + +
142B ILE* 4.5 14.8 - - + -
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Residues in contact with ALA 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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69B SER* 4.2 11.5 + - - -
70B ARG 6.0 0.2 - - - -
71B ALA* 3.6 29.8 - - + -
76B CYS* 3.6 10.9 - - - -
102B VAL* 3.0 19.5 + - + +
103B LYS* 3.4 10.1 - - + +
104B PHE 3.2 0.2 - - - -
105B ALA* 1.3 76.3 - - - +
107B ASN* 1.3 62.8 + - - +
108B ILE 3.5 1.3 - - - +
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Residues in contact with ASN 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 LYS* 2.9 44.2 + - - +
104B PHE* 2.9 11.9 + - + +
106B ALA* 1.3 81.0 - - - +
108B ILE* 1.3 66.8 - - - +
109B ASN* 3.0 12.3 + - - +
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Residues in contact with ILE 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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66B VAL* 3.8 24.1 - - + +
69B SER* 4.6 6.8 + - - -
78B LEU* 5.0 2.2 - - + -
104B PHE* 3.2 28.2 + - + +
105B ALA* 3.2 29.3 + - - +
106B ALA 4.8 0.9 - - - +
107B ASN* 1.3 76.8 - - - +
109B ASN* 1.3 74.1 + - - +
110B LYS* 3.5 2.3 + - - +
112B SER* 3.6 19.7 - - - +
114B VAL* 4.0 2.7 - - + -
142B ILE* 3.7 25.4 - - + -
144B VAL* 3.8 24.2 - - + -
147B LEU* 5.1 3.8 - - + -
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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