Contacts of the helix formed by residues 11 - 20 (chain P) in PDB entry 3H1J
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 11 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ILE* 4.3 35.0 - - + -
199C THR* 5.1 9.4 - - + -
200C PHE* 3.9 22.2 - - + -
9P HIS* 2.7 27.4 + - + -
10P PRO* 1.3 78.1 - - + +
12P LEU* 1.3 63.4 + - + +
13P LYS 3.1 1.1 - - - -
14P MET* 2.8 36.3 + - - +
15P ILE* 3.1 14.2 - - + +
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Residues in contact with LEU 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P ILE* 3.7 24.2 - - + +
6P ARG* 3.7 11.7 - - + +
9P HIS* 3.3 28.8 + - + +
11P LEU* 1.3 75.8 - - + +
13P LYS* 1.3 55.3 + - - +
14P MET 2.6 16.4 + - - -
15P ILE* 2.9 16.6 + - + +
16P ASN* 2.8 25.5 + - - +
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Residues in contact with LYS 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLU* 5.8 2.8 + - - -
6P ARG 3.5 14.2 + - - -
7P LYS* 3.0 30.3 - - - +
8P SER* 3.4 17.5 + - - +
9P HIS 2.7 19.2 + - - +
10P PRO* 4.3 10.7 - - + +
12P LEU* 1.3 76.4 - - - +
14P MET* 1.3 52.5 + - + +
16P ASN* 4.3 0.7 + - - +
17P ASN* 2.7 48.1 + - - +
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Residues in contact with MET 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C THR* 6.2 2.7 - - - -
10P PRO 3.7 17.7 - - - +
11P LEU* 2.8 22.1 + - - +
12P LEU 2.6 5.1 + - - -
13P LYS* 1.3 76.7 - - + +
15P ILE* 1.3 60.8 + - + +
16P ASN 3.1 1.3 - - - -
17P ASN* 3.5 5.4 - - + +
18P SER* 2.6 35.6 + - - -
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Residues in contact with ILE 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P LEU* 3.1 24.5 - - + +
12P LEU* 2.9 20.2 + - + +
14P MET* 1.3 76.0 - - + +
16P ASN* 1.3 59.6 + - - +
18P SER* 4.1 3.4 - - - -
19P LEU* 2.8 45.4 + - + +
20P ILE* 3.7 15.2 + - + +
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Residues in contact with ASN 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P ARG* 2.8 44.3 + - + +
7P LYS* 4.0 14.3 - - - +
12P LEU* 2.8 14.8 + - + +
13P LYS 4.3 1.2 + - - +
15P ILE* 1.3 78.6 - - - +
17P ASN* 1.3 71.9 + - - +
18P SER 3.3 0.7 + - - -
20P ILE* 3.4 15.0 + - + +
21P ASP* 2.7 69.9 + - - +
2T ILE* 5.8 3.0 - - - +
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Residues in contact with ASN 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P LYS* 2.7 34.9 + - + +
14P MET* 3.1 8.5 + - - +
16P ASN* 1.3 85.0 + - - +
18P SER* 1.3 57.8 + - - +
21P ASP* 5.4 2.0 - - - +
22P LEU* 4.1 20.0 - - - +
202P HIS* 5.3 1.7 + - - -
1T GLY* 3.0 45.9 + - - +
2T ILE* 4.2 11.4 + - - +
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Residues in contact with SER 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P MET 2.6 21.6 + - - -
15P ILE* 3.9 3.6 + - - -
17P ASN* 1.3 81.2 - - - +
19P LEU* 1.3 73.8 + - - +
20P ILE 3.8 0.7 - - - -
22P LEU* 3.1 28.1 - - - +
202P HIS* 3.5 25.1 - - - -
221P PHE* 4.8 0.3 - - - -
2015P UNL 4.6 6.3 - - - -
3002P UQ 3.9 6.9 - - - +
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Residues in contact with LEU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P ILE* 2.8 25.1 + - + +
18P SER* 1.3 89.6 - - - +
20P ILE* 1.3 71.8 + - + +
221P PHE* 3.2 51.8 - - + -
222P HIS* 4.0 4.2 - - - +
226P SER* 5.4 0.5 - - - -
3002P UQ 3.9 43.5 - - + -
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Residues in contact with ILE 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436N ARG* 2.9 37.2 + - - +
6P ARG* 4.7 9.2 - - + +
15P ILE* 3.9 18.2 - - + +
16P ASN* 3.4 25.2 + - + +
18P SER 3.8 0.6 - - - -
19P LEU* 1.3 92.6 - - + +
21P ASP* 1.3 73.3 + - - +
22P LEU 3.3 4.5 - - - +
220P PRO* 3.6 0.5 - - - +
221P PHE 3.6 3.3 + - - -
222P HIS* 3.3 31.0 + - + -
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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