Contacts of the helix formed by residues 9 - 21 (chain X) in PDB entry 3J0S
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 9 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7X VAL* 3.5 15.6 - - - +
8X SER* 1.3 78.6 - - - +
10X GLY* 1.3 61.7 + - - +
11X VAL 3.4 2.4 - - - +
12X ILE* 3.5 15.8 + - - +
13X LYS* 3.2 24.8 + - - +
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Residues in contact with GLY 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X SER* 3.1 16.1 + - - -
9X ASP* 1.3 77.4 - - - +
11X VAL* 1.3 62.1 + - - +
13X LYS* 3.3 10.9 + - - +
14X VAL* 3.2 23.5 + - - +
48X ILE* 4.5 12.8 - - - -
49X LEU* 4.4 14.6 - - - +
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Residues in contact with VAL 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X VAL* 5.8 2.7 - - + -
9X ASP* 3.4 1.2 - - - +
10X GLY* 1.3 74.8 - - - +
12X ILE* 1.3 61.3 + - + +
14X VAL* 3.1 9.7 - - - +
15X PHE* 2.8 33.1 + - + +
38X PHE* 3.5 31.4 - - + -
47X ILE* 3.5 43.5 + - + +
48X ILE 4.2 2.2 - - - +
84X LEU* 5.7 0.7 - - + -
101X PHE* 6.2 0.9 - - + -
127X LYS* 3.1 34.8 - - + +
128X LEU* 5.3 6.1 - - + -
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Residues in contact with ILE 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X VAL* 4.2 24.0 - - + +
9X ASP* 3.5 16.9 + - - +
10X GLY 3.3 0.6 - - - -
11X VAL* 1.3 78.7 - - + +
13X LYS* 1.3 57.3 + - - +
15X PHE* 3.8 7.5 - - + +
16X ASN* 2.8 34.5 + - + +
127X LYS* 5.2 17.7 - - + +
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Residues in contact with LYS 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X ASP* 3.2 19.5 + - - +
10X GLY* 3.4 13.0 - - - +
12X ILE* 1.3 79.3 - - - +
14X VAL* 1.3 61.0 + - - +
16X ASN* 3.7 7.3 + - - +
17X ASP* 3.4 18.7 + - - +
49X LEU* 6.4 1.8 - - + -
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Residues in contact with VAL 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X GLY 3.2 8.0 + - - +
11X VAL 3.1 15.5 - - - +
13X LYS* 1.3 78.7 - - - +
15X PHE* 1.3 65.3 + - - +
17X ASP* 3.2 20.7 + - + +
18X MET* 3.2 8.3 + - - +
33X LYS* 3.7 26.3 - - + -
36X VAL* 4.3 14.6 - - + -
38X PHE* 3.2 29.4 - - + -
49X LEU* 3.9 31.0 - - + -
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Residues in contact with PHE 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ASN* 6.1 0.7 - - - -
11X VAL* 2.8 27.5 + - + +
12X ILE* 3.8 7.2 - - + +
14X VAL* 1.3 74.5 - - + +
16X ASN* 1.3 67.0 + - - +
18X MET* 3.2 25.2 + - + +
19X LYS* 3.0 38.7 + - + +
84X LEU* 3.5 31.9 - - + -
99X LEU* 4.3 17.7 - - + -
128X LEU* 4.7 24.7 - - + -
131X ILE* 5.1 5.8 - - + -
132X LYS* 5.0 7.2 - - - -
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Residues in contact with ASN 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ILE* 2.8 23.9 + - + +
13X LYS* 3.7 8.5 + - - +
14X VAL 3.3 0.2 - - - -
15X PHE* 1.3 80.6 - - - +
17X ASP* 1.3 63.1 + - - +
19X LYS* 3.3 19.5 + - - +
20X VAL* 3.3 27.9 + - - +
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Residues in contact with ASP 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LYS 3.4 9.9 + - - +
14X VAL* 3.2 14.5 - - - +
16X ASN* 1.3 83.2 - - - +
18X MET* 1.3 55.9 + - - +
20X VAL* 3.6 1.0 + - - -
21X ARG* 3.0 30.8 + - - +
22X LYS* 3.2 37.2 + - + +
33X LYS* 3.2 24.5 + - - +
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Residues in contact with MET 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ARG* 2.5 48.1 + - - +
14X VAL 3.2 7.2 + - - +
15X PHE* 3.2 33.7 + - + +
17X ASP* 1.3 80.6 + - - +
19X LYS* 1.3 61.9 + - - +
21X ARG* 3.3 13.1 + - - +
32X ARG* 5.5 4.0 - - + -
33X LYS* 4.0 22.8 - - - +
34X LYS 5.5 0.4 - - - +
36X VAL* 5.4 6.1 - - + -
84X LEU* 4.0 28.5 - - + -
85X TYR 5.6 0.2 - - - -
86X ASP* 3.3 23.8 - - - +
99X LEU* 3.6 30.3 - - + -
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Residues in contact with LYS 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J HIS* 5.2 7.4 + - - -
91J TYR* 3.6 62.4 - - + +
92J ASN* 4.7 12.8 - - - +
95J ARG* 4.1 14.9 + - - +
15X PHE* 3.0 34.5 + - + +
16X ASN* 3.3 19.0 + - - +
18X MET* 1.3 77.7 - - - +
20X VAL* 1.3 60.7 + - + +
21X ARG* 5.2 0.5 - - - +
99X LEU* 5.0 7.0 - - + -
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Residues in contact with VAL 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91J TYR* 4.8 24.0 - - + -
97J ALA* 4.6 14.5 + - + +
99J GLU* 4.8 14.1 - - - +
16X ASN* 3.3 30.4 + - - +
17X ASP* 4.6 0.9 - - - +
19X LYS* 1.3 81.3 - - + +
21X ARG* 1.3 72.2 + - - +
22X LYS* 3.1 15.6 + - + +
23X SER 4.7 0.9 + - - +
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Residues in contact with ARG 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J ARG* 3.4 31.4 + - + +
96J VAL* 4.1 12.5 - - - +
97J ALA* 3.6 33.4 + - - +
100J GLU* 3.5 23.0 + - - -
101J HIS* 5.6 0.6 + - - -
17X ASP* 3.0 14.6 + - - +
18X MET* 3.3 12.9 + - - +
19X LYS 5.2 0.4 - - - +
20X VAL* 1.3 80.0 + - - +
22X LYS* 1.3 69.1 + - - +
23X SER* 3.1 37.9 + - - +
29X VAL* 5.1 7.5 - - - +
32X ARG* 4.0 44.4 - - - +
33X LYS* 5.5 0.2 + - - -
97X GLU* 6.1 0.9 - - - -
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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