Contacts of the helix formed by residues 98 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP* 2.7 28.6 + - - -
24A TYR* 3.3 27.8 + - - -
25A ALA* 3.6 9.2 - - - +
93A VAL* 4.1 3.1 - - - -
97A ALA* 1.3 76.5 - - - +
99A LYS* 1.3 64.8 + - - +
100A GLN* 3.2 14.4 + - - +
101A MET* 3.1 20.4 + - - +
102A VAL* 3.0 22.5 + - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LYS* 6.4 0.4 - - - -
93A VAL* 3.8 23.7 - - + +
98A SER* 1.3 73.9 - - - +
100A GLN* 1.3 83.1 + - + +
102A VAL* 3.7 5.5 - - + +
103A LYS* 3.1 25.9 + - - +
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Residues in contact with GLN 100 (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 GLU* 3.7 21.0 + - - +
23A ASP* 3.8 20.4 - - + +
24A TYR* 5.6 0.3 - - - -
29A TYR* 3.3 22.5 + - - +
98A SER* 3.1 21.0 + - - +
99A LYS* 1.3 100.1 - - - +
101A MET* 1.3 55.8 + - - +
103A LYS* 3.5 10.3 + - + +
104A PHE* 3.0 27.0 + - - +
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Residues in contact with MET 101 (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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25A ALA* 4.2 3.4 - - + -
28A ARG* 3.7 31.9 - - - +
29A TYR* 3.5 34.5 - - + -
91A VAL* 4.6 5.2 - - + -
97A ALA* 3.5 27.8 - - + -
98A SER* 3.1 18.6 + - - +
100A GLN* 1.3 73.4 - - - +
102A VAL* 1.3 66.8 + - - +
104A PHE* 3.2 3.8 + - - +
105A ALA* 2.9 22.7 + - - +
139A VAL* 4.2 7.0 - - + +
140A GLN* 3.3 30.7 - - - +
141A LYS* 3.7 4.9 - - - +
142A ILE* 3.9 15.9 - - + +
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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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71A ALA* 5.4 3.6 - - + -
73A GLY 5.0 3.6 - - - +
74A LYS* 3.7 23.6 - - - +
75A GLN 3.9 28.0 - - - +
76A CYS* 3.9 4.4 - - + +
91A VAL* 4.0 22.7 - - + +
92A ALA 4.2 0.4 - - - -
93A VAL* 3.8 19.7 - - + +
97A ALA* 4.3 1.1 - - + -
98A SER 3.0 13.7 + - - +
99A LYS* 3.7 9.4 - - - +
101A MET* 1.3 76.3 - - - +
103A LYS* 1.3 58.0 + - - +
105A ALA* 3.2 4.9 + - - +
106A ALA* 2.9 27.1 + - + +
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Residues in contact with LYS 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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99A LYS 3.1 15.2 + - - +
100A GLN* 3.7 9.2 - - + +
101A MET 3.2 0.2 - - - -
102A VAL* 1.3 77.8 - - - +
104A PHE* 1.3 66.3 + - - +
106A ALA* 3.3 6.4 + - - +
107A ASN* 2.7 44.4 + - - +
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Residues in contact with PHE 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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29A TYR* 3.5 30.7 - + + -
30A GLY* 3.1 44.6 - - - -
31A ILE* 3.5 22.2 - - + -
100A GLN 3.0 15.1 + - - +
101A MET 3.2 8.7 + - - +
103A LYS* 1.3 76.0 - - - +
105A ALA* 1.3 67.1 + - - +
107A ASN* 3.1 14.1 + - - +
108A ILE* 3.3 32.0 + - + +
142A ILE* 4.2 10.8 - - + -
144A VAL* 4.0 12.6 - - + -
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Residues in contact with ALA 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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69A SER* 3.9 7.6 + - - -
76A CYS* 3.9 7.4 - - - -
78A LEU* 4.1 8.8 - - + +
91A VAL* 3.8 29.8 - - + -
101A MET 2.9 12.7 + - - +
102A VAL 3.4 8.3 - - - +
104A PHE* 1.3 78.8 - - - +
106A ALA* 1.3 61.7 + - - +
107A ASN 3.0 1.4 + - - -
108A ILE* 3.2 32.4 + - + +
142A ILE* 4.6 9.0 - - + -
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Residues in contact with ALA 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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69A SER* 4.0 13.6 + - - -
70A ARG 5.3 0.4 - - - -
71A ALA* 3.6 30.1 - - + +
76A CYS* 3.5 12.5 - - - -
102A VAL* 2.9 16.3 + - + +
103A LYS* 3.7 9.0 - - - +
104A PHE 3.3 0.4 - - - -
105A ALA* 1.3 74.9 - - - +
107A ASN* 1.3 64.7 + - - +
108A ILE 3.6 1.1 - - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 2.7 41.2 + - - +
104A PHE* 3.1 7.0 + - - +
105A ALA 3.0 1.0 + - - -
106A ALA* 1.3 85.7 - - - +
108A ILE* 1.3 63.6 + - - +
109A ASN* 3.2 12.5 + - - +
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Residues in contact with ILE 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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66A VAL* 3.7 25.4 - - + +
69A SER* 5.2 4.5 - - - -
78A LEU* 5.0 0.9 - - + -
104A PHE* 3.3 24.4 + - + +
105A ALA* 3.2 23.3 + - - +
106A ALA 4.9 1.7 - - - +
107A ASN* 1.3 77.4 - - - +
109A ASN* 1.3 68.1 + - - +
110A LYS* 3.4 2.6 + - - +
112A SER* 3.5 28.0 - - - +
114A VAL* 4.1 3.4 - - + -
142A ILE* 3.7 29.6 - - + -
144A VAL* 3.8 28.7 - - + -
147A LEU* 5.1 3.6 - - + -
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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