Contacts of the helix formed by residues 7 - 21 (chain C) in PDB entry 1JIQ
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 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ALA 3.2 10.7 + - - +
4C LEU 3.1 16.1 + - - +
5C THR 3.2 0.2 - - - -
6C ARG* 1.3 76.2 - - - +
8C PRO* 1.3 64.0 - - - +
9C GLN* 2.8 34.1 + - - +
10C PHE* 3.1 11.6 + - + +
11C GLN* 2.9 30.0 + - - +
71C LEU* 3.5 5.2 - - - +
74C SER* 2.4 28.8 + - - +
75C ARG* 3.6 24.7 + - - -
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Residues in contact with PRO 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ALA 6.0 0.7 - - - +
234A LYS* 4.0 36.1 - - + -
6C ARG 3.5 8.0 - - - +
7C ASP* 1.3 94.7 - - - +
9C GLN* 1.3 69.7 + - - +
11C GLN* 3.2 12.6 + - + +
12C LYS* 2.9 27.9 + - - +
74C SER* 4.4 4.9 - - - +
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Residues in contact with GLN 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASP* 2.8 12.0 + - - +
8C PRO* 1.3 84.2 - - - +
10C PHE* 1.3 65.8 + - - +
12C LYS* 2.9 40.5 + - - +
13C LEU* 3.0 23.2 + - - +
67C MET 4.7 2.0 - - - +
70C ASP* 3.5 27.4 - - + +
71C LEU* 3.8 20.6 - - + +
74C SER* 3.6 16.8 - - - +
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Residues in contact with PHE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.3 57.2 - - + +
5C THR* 4.0 22.2 - - + -
7C ASP* 3.1 8.6 + - + +
9C GLN* 1.3 79.3 - - - +
11C GLN* 1.3 57.2 + - - +
13C LEU* 3.0 13.3 + - + +
14C GLN* 2.9 71.1 + - + +
71C LEU* 3.7 19.0 - - + +
325C ILE* 5.0 2.2 - - + -
329C ASN* 3.8 37.0 - - + -
330C CYS* 4.6 8.5 - - - -
373C HIS* 5.6 2.9 - - + -
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Residues in contact with GLN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLN* 4.8 8.1 - - - +
234A LYS* 4.7 15.0 - - - +
5C THR 3.0 23.4 - - - +
6C ARG* 3.9 12.9 - - - +
7C ASP 2.9 21.6 + - - +
8C PRO* 3.6 9.3 - - + +
10C PHE* 1.3 76.4 - - + +
12C LYS* 1.3 63.2 + - - +
14C GLN* 3.3 18.1 + - - +
15C GLN* 3.0 23.4 + - - +
18C ARG* 4.9 1.7 + - - -
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Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO 2.9 10.8 + - - +
9C GLN* 2.9 45.7 + - - +
11C GLN* 1.3 72.9 - - - +
13C LEU* 1.3 65.8 + - - +
15C GLN* 3.4 7.8 + - - +
16C TRP* 2.9 24.8 + - - +
66C ARG* 3.6 18.6 - - - +
67C MET* 3.6 32.8 - - - +
70C ASP* 3.2 23.9 + - - -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLN 3.0 13.8 + - - +
10C PHE* 3.0 17.2 + - + +
12C LYS* 1.3 77.9 - - - +
14C GLN* 1.3 62.5 + - - +
16C TRP* 3.2 4.3 + - - +
17C TYR* 2.9 23.0 + - - +
64C VAL* 4.5 2.5 - - + -
67C MET* 3.9 38.1 - - + +
68C LEU* 3.4 33.2 - - + -
71C LEU* 4.5 14.6 - - + -
325C ILE* 5.1 4.7 - - + -
326C TRP* 3.4 36.0 - - + -
330C CYS* 4.1 11.4 - - - -
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Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 4.9 3.0 - - - +
10C PHE* 2.9 54.5 + - + +
11C GLN* 3.5 22.8 - - - +
13C LEU* 1.3 78.4 - - - +
15C GLN* 1.3 63.1 + - - +
17C TYR* 3.1 9.5 + - - +
18C ARG* 2.9 45.5 + - - +
329C ASN 5.1 4.2 + - - -
330C CYS* 4.5 8.7 - - - -
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Residues in contact with GLN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLN 3.0 13.9 + - - +
12C LYS* 3.6 8.5 - - - +
14C GLN* 1.3 79.5 - - - +
16C TRP* 1.3 65.9 + - - +
18C ARG* 3.2 31.1 + - - +
19C GLU* 2.5 65.8 + - - +
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS 2.9 17.7 + - - +
13C LEU 3.2 4.5 + - - +
15C GLN* 1.3 79.2 - - - +
17C TYR* 1.3 60.9 + - - +
19C GLU 3.1 0.5 + - - -
20C HIS* 2.8 83.1 + + + -
21C ARG 4.3 0.9 - - - -
23C GLU* 4.2 12.3 - - + -
24C LEU* 3.9 33.0 - - + -
61C THR* 4.2 9.9 - - + -
63C ASP* 4.6 13.6 + - + +
64C VAL* 3.6 25.1 - - + -
67C MET* 3.3 32.9 - - + +
326C TRP* 4.0 11.2 - + - -
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU 2.9 13.4 + - - +
14C GLN* 3.1 13.2 + - - +
16C TRP* 1.3 86.7 - - - +
18C ARG* 1.3 71.6 + - + +
21C ARG* 2.7 74.7 + - + +
326C TRP* 3.9 18.2 - + + -
330C CYS* 3.5 38.3 + - + -
331C PHE* 3.6 42.2 + + - -
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLN 4.9 1.4 + - - -
14C GLN* 2.9 42.3 + - + +
15C GLN* 3.4 40.6 - - - +
17C TYR* 1.3 89.6 - - + +
19C GLU* 1.3 62.9 + - + +
21C ARG* 5.0 4.0 + - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLN* 2.5 49.2 + - - +
16C TRP* 5.0 0.2 - - - -
18C ARG* 1.3 82.2 - - + +
20C HIS* 1.3 88.0 + - + +
21C ARG 3.9 0.2 - - - -
22C SER* 4.7 4.7 + - - -
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Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 2.8 75.9 + + + +
19C GLU* 1.3 101.6 + - + +
21C ARG* 1.3 58.2 + - - +
22C SER* 2.7 14.9 + - - -
23C GLU* 2.9 41.4 + - - +
24C LEU 4.1 0.2 + - - -
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Residues in contact with ARG 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TRP* 4.1 1.7 + - - -
17C TYR* 2.7 71.0 + - + +
18C ARG* 5.0 3.8 + - - +
19C GLU 3.9 0.6 - - - -
20C HIS* 1.3 75.0 - - - +
22C SER* 1.3 62.0 + - - +
23C GLU 3.3 0.2 - - - -
24C LEU* 3.2 40.4 + - + +
59C LEU* 5.6 1.4 - - - +
331C PHE* 3.6 24.5 - - + -
401C MET* 4.8 7.9 - - - +
471C ASN* 5.9 2.8 - - - +
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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