Contacts of the helix formed by residues 9 - 21 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7U VAL* 3.5 14.7 - - - +
8U SER* 1.3 79.2 - - - +
10U GLY* 1.3 62.4 + - - +
11U VAL 3.4 2.4 - - - +
12U ILE* 3.5 15.3 + - - +
13U LYS* 3.2 24.1 + - - +
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Residues in contact with GLY 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U SER* 3.1 15.5 + - - -
9U ASP* 1.3 76.8 - - - +
11U VAL* 1.3 60.8 + - - +
13U LYS* 3.3 11.3 + - - +
14U VAL* 3.2 23.3 + - - +
48U ILE* 4.5 12.1 - - - -
49U LEU* 4.4 14.5 - - - +
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Residues in contact with VAL 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U VAL* 5.8 2.5 - - + -
9U ASP 3.4 0.6 - - - +
10U GLY* 1.3 75.0 - - - +
12U ILE* 1.3 61.1 + - + +
14U VAL* 3.1 9.3 - - - +
15U PHE* 2.8 33.3 + - + +
38U PHE* 3.5 31.2 - - + -
47U ILE* 3.5 42.8 + - + +
48U ILE* 4.2 2.7 - - - +
84U LEU* 5.7 1.1 - - + -
101U PHE* 6.2 0.7 - - + -
127U LYS* 3.1 35.0 - - + +
128U LEU* 5.3 6.3 - - + -
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Residues in contact with ILE 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U VAL* 4.2 24.2 - - + -
9U ASP* 3.5 16.7 + - - +
10U GLY 3.3 0.6 - - - -
11U VAL* 1.3 79.3 - - + +
13U LYS* 1.3 58.3 + - - +
15U PHE* 3.8 7.5 - - + +
16U ASN* 2.8 33.8 + - + +
127U LYS* 5.2 17.5 - - + +
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Residues in contact with LYS 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U ASP* 3.2 18.8 + - - +
10U GLY* 3.4 13.0 - - - +
12U ILE* 1.3 79.1 - - - +
14U VAL* 1.3 62.2 + - - +
16U ASN* 3.7 6.9 + - - +
17U ASP* 3.4 18.9 + - - +
49U LEU* 6.4 2.0 - - + -
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Residues in contact with VAL 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U GLY 3.2 8.6 + - - +
11U VAL 3.1 15.0 - - - +
13U LYS* 1.3 77.9 - - - +
15U PHE* 1.3 65.3 + - - +
17U ASP* 3.2 20.4 + - + +
18U MET* 3.2 8.8 + - - +
33U LYS* 3.7 27.0 - - + -
36U VAL* 4.3 13.9 - - + -
38U PHE* 3.2 28.3 - - + -
49U LEU* 3.9 31.9 - - + -
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Residues in contact with PHE 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ASN* 6.1 0.9 - - - -
11U VAL* 2.8 27.8 + - + +
12U ILE* 3.8 6.7 - - + +
14U VAL* 1.3 75.2 - - - +
16U ASN* 1.3 65.8 + - + +
18U MET* 3.2 26.2 + - + +
19U LYS* 3.0 39.2 + - + +
84U LEU* 3.5 32.8 - - + -
99U LEU* 4.3 17.7 - - + -
128U LEU* 4.7 23.6 - - + -
131U ILE* 5.1 6.3 - - + -
132U LYS* 5.0 6.7 - - - -
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Residues in contact with ASN 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ILE* 2.8 24.2 + - + +
13U LYS* 3.7 7.8 + - - +
15U PHE* 1.3 79.9 - - - +
17U ASP* 1.3 64.3 + - - +
19U LYS* 3.3 20.1 + - - +
20U VAL* 3.3 28.4 + - - +
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Residues in contact with ASP 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U LYS 3.4 9.8 + - - +
14U VAL* 3.2 15.6 + - - +
16U ASN* 1.3 82.3 - - - +
18U MET* 1.3 56.6 + - - +
20U VAL* 3.6 1.2 + - - +
21U ARG* 3.0 30.5 + - - +
22U LYS* 3.2 36.8 + - + +
33U LYS* 3.2 24.4 + - - +
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Residues in contact with MET 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ARG* 2.5 47.3 + - - +
14U VAL 3.2 7.8 + - - +
15U PHE* 3.2 33.7 + - + +
17U ASP* 1.3 80.2 + - - +
19U LYS* 1.3 61.2 + - - +
21U ARG* 3.3 12.9 + - - +
32U ARG* 5.5 4.0 - - + -
33U LYS* 4.0 22.8 - - - +
34U LYS 5.5 0.7 - - - +
36U VAL* 5.4 6.3 - - + -
84U LEU* 4.0 27.8 - - + -
85U TYR 5.6 0.4 - - - -
86U ASP* 3.3 23.6 - - - +
99U LEU* 3.6 30.3 - - + -
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Residues in contact with LYS 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F HIS* 5.2 7.8 + - - -
91F TYR* 3.6 59.8 - - + +
92F ASN* 4.7 14.5 - - - +
95F ARG* 4.1 15.3 + - - +
15U PHE* 3.0 35.5 + - + +
16U ASN* 3.3 19.4 + - - +
18U MET* 1.3 79.5 - - - +
20U VAL* 1.3 62.5 + - + +
21U ARG* 3.9 0.7 + - - +
99U LEU* 5.0 6.3 - - + -
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Residues in contact with VAL 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F TYR* 4.8 23.1 - - + -
97F ALA* 4.6 15.3 + - + +
99F GLU* 4.8 13.2 - - - +
16U ASN* 3.3 29.8 + - - +
17U ASP* 4.6 0.9 - - - +
19U LYS* 1.3 81.6 - - + +
21U ARG* 1.3 71.6 + - - +
22U LYS* 3.1 15.5 + - + +
23U SER 4.7 1.2 + - - +
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Residues in contact with ARG 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ARG* 3.4 31.4 + - + +
96F VAL* 4.1 13.2 - - - +
97F ALA* 3.6 34.4 + - - +
100F GLU* 3.5 23.0 + - - -
101F HIS* 5.6 0.2 + - - -
17U ASP* 3.0 15.2 + - - +
18U MET* 3.3 12.5 + - - +
19U LYS 5.2 0.4 - - - +
20U VAL* 1.3 79.7 + - - +
22U LYS* 1.3 68.8 + - - +
23U SER* 3.1 38.1 + - - +
24U SER* 5.9 0.2 - - - +
29U VAL* 5.1 7.3 - - - +
32U ARG* 4.0 43.5 - - - +
33U LYS* 5.5 0.3 + - - -
97U 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