Contacts of the helix formed by residues 7 - 18 (chain C) in PDB entry 4JRI
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 LEU 7 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLN 2.7 10.5 + - - +
6C SER* 1.3 68.9 - - - +
8C GLN* 1.3 60.5 + - - -
9C ASP 3.4 0.4 - - - -
10C PRO* 3.7 13.2 - - + +
11C PHE* 3.4 20.8 + - + +
38D SER* 3.2 31.0 - - - +
39D TRP* 4.1 18.8 - - - +
40D ASP* 2.6 17.4 + - + +
43D VAL* 4.1 12.3 - - + -
45D LEU* 3.5 35.2 - - + -
53D MET* 5.0 0.2 - - - +
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Residues in contact with GLN 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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6C SER* 2.8 8.2 + - - +
7C LEU* 1.3 80.0 - - - +
9C ASP* 1.3 67.4 + - - +
11C PHE* 3.4 2.1 + - - +
12C LEU* 3.1 34.4 + - + +
56C LYS* 2.8 30.1 + - - +
40D ASP* 3.4 7.1 + - - +
42D PHE* 4.2 24.9 - - - +
43D VAL* 4.1 6.2 - - + +
53D MET* 3.8 26.2 - - + -
55D TYR* 2.5 38.0 + - - +
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Residues in contact with ASP 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.0 26.0 + - - +
8C GLN* 1.3 79.5 + - - +
10C PRO* 1.4 66.8 - - + +
12C LEU 3.4 0.3 + - - -
13C ASN* 2.8 36.6 + - - +
39C TRP* 3.1 34.7 + - + +
56C LYS* 5.1 3.1 + - - -
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Residues in contact with PRO 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 3.2 13.9 - - - +
7C LEU* 3.7 20.4 - - + +
9C ASP* 1.4 92.6 - - + +
11C PHE* 1.3 58.7 + - - +
13C ASN* 3.7 7.7 - - + +
14C ALA* 3.0 25.3 + - - +
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Residues in contact with PHE 11 (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 LEU* 3.4 18.4 + - + +
8C GLN 3.7 3.4 - - - +
9C ASP 3.3 0.8 - - - -
10C PRO* 1.3 78.0 - - - +
12C LEU* 1.3 64.3 + - + +
14C ALA* 3.5 5.0 + - - +
15C LEU* 3.3 46.4 + - + +
62C VAL* 4.1 10.8 - - + -
64C PRO* 3.8 17.3 - - + -
68C VAL* 4.7 12.2 - - + +
45D LEU* 4.1 27.4 - - + -
51D SER* 3.7 26.5 - - - -
53D MET* 3.6 47.8 - - + -
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.1 39.0 + - + +
11C PHE* 1.3 74.9 - - + +
13C ASN* 1.3 60.4 + - - +
15C LEU* 3.3 16.6 + - + +
16C ARG* 3.0 28.6 + - - +
36C ILE* 4.1 26.9 - - + +
39C TRP* 3.7 48.0 - - + -
44C ILE* 4.2 20.4 - - + -
62C VAL* 4.6 5.2 - - + -
53D MET* 4.1 20.2 - - + -
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Residues in contact with ASN 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 ASP* 2.8 25.0 + - - +
10C PRO* 3.7 8.6 - - + +
12C LEU* 1.3 76.7 - - - +
14C ALA* 1.3 57.1 + - - +
16C ARG* 2.8 35.9 + - - +
17C ARG* 2.8 45.2 + - - +
39C TRP* 3.4 18.3 - - - -
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Residues in contact with ALA 14 (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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10C PRO 3.0 17.5 + - - +
11C PHE* 3.8 5.6 - - - +
12C LEU 3.3 0.2 - - - -
13C ASN* 1.3 75.8 - - - +
15C LEU* 1.3 60.9 + - - +
17C ARG* 4.1 19.2 + - - +
18C GLU* 3.6 26.2 + - - +
20C VAL* 4.7 0.5 - - - +
68C VAL* 3.4 29.9 - - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 3.3 41.5 + - + +
12C LEU* 3.3 14.3 + - + +
13C ASN 3.2 0.2 - - - -
14C ALA* 1.3 76.7 - - - +
16C ARG* 1.3 62.2 + - - +
19C ARG* 3.2 2.6 + - - -
20C VAL* 2.9 43.5 + - + +
22C VAL* 3.8 28.5 - - + -
35C GLN* 5.8 0.3 - - - +
36C ILE* 4.4 8.0 + - + +
62C VAL* 4.3 11.2 - - + -
64C PRO* 3.6 31.9 - - + -
68C VAL* 4.1 14.8 - - + -
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Residues in contact with ARG 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 LEU 3.0 17.3 + - - +
13C ASN* 2.8 29.1 + - - +
15C LEU* 1.3 76.4 - - - +
17C ARG* 1.3 88.6 + - - +
19C ARG* 3.1 20.7 + - - +
35C GLN* 5.7 0.4 - - - +
36C ILE* 3.5 29.2 - - + +
37C GLU* 3.5 22.0 - - - +
38C SER* 4.8 0.9 - - - +
39C TRP* 3.7 20.4 - - + -
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Residues in contact with ARG 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 ASN* 2.8 30.3 + - - +
14C ALA* 4.1 18.9 - - - +
16C ARG* 1.3 99.0 - - - +
18C GLU* 1.3 74.1 + - + +
19C ARG* 3.1 11.8 + - - +
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Residues in contact with GLU 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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14C ALA 3.6 17.3 + - - +
16C ARG 3.4 0.4 - - - -
17C ARG* 1.3 95.5 + - + +
19C ARG* 1.3 70.5 + - - +
20C VAL* 3.0 14.6 + - + -
66C ARG* 3.9 16.6 + - - +
68C VAL* 6.3 2.2 - - + -
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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