Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 1J7D
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 PRO 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS 3.7 0.9 - - - +
9A VAL* 1.3 92.0 - - + +
11A ARG* 1.3 66.8 + - - +
12A ASN 4.6 0.9 - - - +
13A PHE* 3.0 12.9 + - + -
14A ARG* 2.9 19.2 + - - +
31B ASN* 3.9 10.3 - - - +
34B TYR* 3.6 48.7 - - + +
57B PHE* 3.3 38.4 - - + -
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Residues in contact with ARG 11 (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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9A VAL 3.6 1.2 + - - -
10A PRO* 1.3 70.1 - - - +
12A ASN* 1.3 85.1 + - - +
14A ARG* 3.1 2.3 + - - +
15A LEU* 2.9 48.1 + - + +
42A THR* 2.9 20.0 + - - +
44A THR* 3.0 26.3 + - - +
69A CYS 2.7 23.0 + - - -
70A GLY 2.7 27.6 + - - -
71A PRO* 3.4 20.1 - - - +
73A TYR* 3.0 24.1 + - - +
74A PRO* 4.1 8.8 - - - +
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Residues in contact with ASN 12 (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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10A PRO* 3.3 1.2 - - - +
11A ARG* 1.3 112.9 + - - +
13A PHE* 1.3 59.8 + - + +
15A LEU* 3.6 3.9 + - - +
16A LEU* 3.1 26.7 + - - +
42A THR* 4.3 2.9 - - - +
43A LEU* 3.7 9.2 - - - +
34B TYR* 3.4 10.7 + - - +
55B GLU* 2.7 41.8 + - - +
70B ARG* 3.5 17.0 + - - +
72B MET* 4.0 11.6 - - - +
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Residues in contact with PHE 13 (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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9A VAL* 3.8 15.0 - - + -
10A PRO* 3.0 21.9 + - + +
12A ASN* 1.3 77.4 - - - +
14A ARG* 1.3 65.5 + - - +
16A LEU* 3.4 20.4 + - + +
17A GLU* 3.1 27.0 + - - +
34B TYR* 3.9 8.7 - + - -
55B GLU* 3.5 41.3 - - + -
57B PHE* 3.6 29.8 - - + -
68B LYS* 3.4 48.9 - - + -
69B VAL* 3.9 8.7 - - - -
70B ARG* 4.4 8.5 - - + -
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Residues in contact with ARG 14 (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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9A VAL* 3.7 12.9 - - + +
10A PRO 2.9 12.3 + - - +
11A ARG 3.5 8.1 - - - +
13A PHE* 1.3 76.9 - - - +
15A LEU* 1.3 60.0 + - - +
17A GLU* 3.0 26.8 + - - +
18A GLU* 2.9 56.4 + - - +
73A TYR* 3.7 7.9 + - + -
74A PRO* 3.7 28.0 - - + +
111A ASN 2.6 30.5 + - - -
112A SER* 3.7 10.1 + - - +
113A TYR 2.8 24.0 + - - -
114A SER* 3.9 3.3 - - - -
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Residues in contact with LEU 15 (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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11A ARG* 2.9 55.6 + - + +
12A ASN* 3.9 0.9 - - - +
14A ARG* 1.3 73.6 - - - +
16A LEU* 1.3 60.6 + - - +
18A GLU* 3.1 11.4 + - - +
19A LEU* 2.8 29.3 + - - +
43A LEU* 3.4 38.8 - - + +
46A TRP* 3.7 19.2 - - + -
69A CYS* 3.9 18.6 - - + -
73A TYR* 3.4 31.0 - - + -
115A ILE* 4.7 0.4 - - + -
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Residues in contact with LEU 16 (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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12A ASN 3.1 16.9 + - - +
13A PHE* 3.5 30.1 - - + +
14A ARG 3.2 0.2 - - - -
15A LEU* 1.3 76.1 - - - +
17A GLU* 1.3 62.8 + - + +
19A LEU* 3.3 18.6 + - + +
20A GLU* 3.1 28.9 + - + +
43A LEU* 4.0 12.5 - - + +
68B LYS* 6.2 2.5 - - + -
69B VAL 5.7 1.1 - - - +
70B ARG* 3.9 29.4 - - + +
83B LEU* 5.3 2.2 - - + -
85B ARG* 3.8 35.4 - - + -
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Residues in contact with GLU 17 (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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9A VAL* 4.2 19.7 - - - +
13A PHE* 3.2 14.8 - - - +
14A ARG* 3.0 28.6 + - - +
16A LEU* 1.3 78.6 - - + +
18A GLU* 1.3 58.8 + - + +
20A GLU* 3.2 8.2 + - - +
21A GLU* 2.9 28.7 + - - +
68B LYS* 5.2 16.4 + - - +
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Residues in contact with GLU 18 (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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14A ARG* 2.9 37.3 + - - +
15A LEU* 3.1 11.3 + - + +
17A GLU* 1.3 76.0 - - + +
19A LEU* 1.3 57.4 + - - +
21A GLU* 4.4 11.7 - - - +
22A GLY 2.9 12.5 + - - -
33A TRP* 2.8 32.4 + - + +
46A TRP* 4.1 7.9 - - + -
73A TYR* 2.5 31.7 + - - -
114A SER* 3.3 14.5 - - - -
115A ILE* 2.9 38.7 + - + +
116A LYS 4.3 1.0 + - - -
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Residues in contact with LEU 19 (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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15A LEU 2.8 13.6 + - - +
16A LEU* 3.3 19.7 - - + +
17A GLU 3.2 0.2 - - - -
18A GLU* 1.3 76.5 - - - +
20A GLU* 1.3 62.2 + - - +
22A GLY* 3.3 2.4 + - - -
23A GLN* 3.1 41.1 + - + +
34A GLY* 5.4 1.8 - - - -
35A LEU* 4.0 25.8 - - + +
43A LEU* 4.8 4.3 - - + -
46A TRP* 3.6 25.1 - - + -
83B LEU* 3.4 29.4 - - + -
85B ARG* 3.7 24.7 - - - +
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Residues in contact with GLU 20 (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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16A LEU* 3.1 15.4 + - + +
17A GLU* 3.2 8.9 + - - +
19A LEU* 1.3 77.0 - - - +
21A GLU* 1.3 61.5 + - - +
23A GLN* 3.2 18.6 + - - +
24A LYS* 3.0 49.8 + - - +
85B ARG* 3.1 30.7 + - - +
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Residues in contact with GLU 21 (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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17A GLU 2.9 16.2 + - - +
18A GLU* 3.9 10.9 - - - +
20A GLU* 1.3 75.6 - - - +
22A GLY* 1.3 58.0 + - - +
24A LYS* 3.2 9.6 + - + +
25A GLY* 2.8 28.5 + - - +
26A VAL* 3.0 31.0 - - + +
33A TRP* 3.7 17.0 - - + -
116A LYS* 3.3 27.9 + - - +
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Residues in contact with GLY 22 (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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18A GLU 2.9 12.4 + - - -
19A LEU 3.7 1.8 - - - -
21A GLU* 1.3 78.6 - - - +
23A GLN* 1.3 59.7 + - - +
25A GLY* 3.3 11.0 + - - -
32A SER* 4.6 7.8 + - - -
33A TRP* 3.3 46.3 + - - +
46A TRP* 6.0 0.2 - - - -
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Residues in contact with GLN 23 (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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19A LEU* 3.1 33.2 + - + +
20A GLU* 3.2 27.0 + - - +
22A GLY* 1.3 79.1 - - - +
24A LYS* 1.3 62.7 + - + +
25A GLY 3.6 0.2 + - - -
85B ARG* 4.7 12.4 + - - +
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Residues in contact with LYS 24 (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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20A GLU* 3.0 41.2 + - - +
21A GLU* 3.8 8.1 - - + +
23A GLN* 1.3 79.9 - - + +
25A GLY* 1.3 67.6 + - - +
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Residues in contact with GLY 25 (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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21A GLU* 2.8 11.5 + - - +
22A GLY* 3.3 8.5 + - - -
23A GLN 3.2 3.2 - - - -
24A LYS* 1.3 87.5 - - - +
26A VAL* 1.3 70.0 + - - +
29A GLY* 6.4 0.7 - - - -
31A VAL 6.1 0.2 - - - -
32A SER* 6.0 1.1 - - - -
33A TRP* 5.5 2.7 - - - -
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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