Contacts of the helix formed by residues 11 - 22 (chain i) in PDB entry 5JPQ
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 ILE 11 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10i ARG* 1.3 81.6 - - + +
12i PRO* 1.3 56.3 - - - +
14i LEU* 3.0 10.7 + - + +
15i ILE* 2.8 29.1 + - - +
48i MET* 6.3 0.7 - - - -
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Residues in contact with PRO 12 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10i ARG* 3.1 6.0 - - - +
11i ILE* 1.3 78.1 - - - +
13i THR* 1.3 61.3 + - - +
15i ILE* 3.3 14.9 + - + +
16i ARG* 3.4 10.2 + - - +
47i SER* 4.3 24.5 - - - +
48i MET* 5.2 5.1 - - + -
49i ASP 5.6 1.6 - - - +
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Residues in contact with THR 13 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10i ARG 3.0 11.5 + - - +
12i PRO* 1.3 76.0 - - - +
14i LEU* 1.3 65.0 + - - +
16i ARG* 2.9 24.1 + - - +
17i ASN* 3.3 5.4 + - - +
214i GLY* 4.4 1.1 - - - -
215i LYS* 3.1 43.7 - - - -
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Residues in contact with LEU 14 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10i ARG 3.4 1.8 + - - -
11i ILE* 3.0 18.1 + - + +
13i THR* 1.3 79.6 - - - +
15i ILE* 1.3 61.5 + - - +
17i ASN* 3.1 10.0 + - - +
18i GLY* 3.0 18.0 + - - -
212i SER 5.5 1.8 - - - +
213i GLY* 4.6 1.8 - - - -
214i GLY* 3.5 29.5 - - - +
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Residues in contact with ILE 15 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11i ILE 2.8 12.6 + - - +
12i PRO* 3.6 13.2 - - + +
13i THR 3.1 0.4 - - - -
14i LEU* 1.3 77.5 - - - +
16i ARG* 1.3 60.2 + - - +
18i GLY* 3.1 3.3 + - - +
19i LEU* 3.1 22.9 + - - +
48i MET* 5.5 10.8 - - + -
49i ASP 5.8 3.1 - - - +
50i VAL* 5.6 13.6 - - + +
146i GLY 4.4 15.8 - - - +
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Residues in contact with ARG 16 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12i PRO 3.4 6.6 + - - +
13i THR* 2.9 14.5 + - - +
15i ILE* 1.3 77.2 - - - +
17i ASN* 1.3 65.6 + - - +
19i LEU* 3.5 4.1 + - - +
20i GLN* 3.2 21.7 + - - +
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Residues in contact with ASN 17 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13i THR 3.3 5.1 + - - +
14i LEU* 3.1 14.6 + - - +
16i ARG* 1.3 78.9 - - - +
18i GLY* 1.3 62.5 + - - +
20i GLN* 3.1 8.2 + - - +
21i THR* 3.0 24.2 + - - -
214i GLY 6.0 1.8 - - - +
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Residues in contact with GLY 18 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14i LEU 3.0 12.8 + - - -
15i ILE* 3.1 4.6 + - - -
17i ASN* 1.3 76.9 - - - +
19i LEU* 1.3 62.3 + - - +
21i THR* 3.2 5.9 + - - -
22i LYS 2.9 17.3 + - - -
23i LYS* 3.0 26.5 + - - -
146i GLY* 3.9 2.5 - - - -
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Residues in contact with LEU 19 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15i ILE 3.1 12.8 + - - +
16i ARG* 3.5 4.2 + - - +
18i GLY* 1.3 75.8 - - - +
20i GLN* 1.3 63.1 + - - +
22i LYS* 3.1 11.7 + - - +
50i VAL* 5.4 9.6 - - + -
145i GLY* 5.3 1.1 - - - -
146i GLY* 3.3 29.2 + - - +
226i ASP 5.7 0.3 - - - +
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Residues in contact with GLN 20 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16i ARG 3.2 12.9 + - - +
17i ASN* 3.1 12.8 + - - +
19i LEU* 1.3 80.1 - - - +
21i THR* 1.3 56.2 + - - +
22i LYS 3.5 0.3 + - - -
225i GLU* 3.6 11.5 - - + +
226i ASP 3.1 24.3 + - - +
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Residues in contact with THR 21 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17i ASN 3.0 14.9 + - - -
18i GLY* 3.2 8.0 + - - -
20i GLN* 1.3 74.7 - - - +
22i LYS* 1.3 68.2 + - - +
23i LYS* 4.1 10.6 - - - +
223i PRO* 3.9 28.5 - - - +
224i ASP 3.9 11.5 - - - +
225i GLU* 4.8 0.2 - - - +
226i ASP* 3.0 13.5 - - - +
481i ALA* 3.4 8.0 - - - +
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Residues in contact with LYS 22 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18i GLY 2.9 5.6 + - - -
19i LEU 3.1 12.8 + - - +
20i GLN 3.2 0.4 - - - -
21i THR* 1.3 81.6 - - - +
23i LYS* 1.3 58.9 + - - +
145i GLY* 4.4 13.6 - - - -
226i ASP* 3.5 20.9 - - + +
479i ARG 5.2 1.3 - - - +
480i TYR* 3.3 15.3 - - - +
481i ALA* 3.1 27.3 + - - +
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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