Contacts of the helix formed by residues 21 - 30 (chain P) in PDB entry 1HI0
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 ASN 21 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P ALA* 2.8 19.8 + - + +
20P ASN* 1.3 74.4 - - - +
22P ILE* 1.3 67.1 + - - +
23P LYS* 2.8 24.3 + - - +
24P ALA* 2.9 16.8 + - - +
25P GLN* 3.1 25.7 + - - +
155P TYR* 3.1 27.6 + - - +
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Residues in contact with ILE 22 (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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21P ASN* 1.3 74.2 + - - +
23P LYS* 1.3 56.0 + - + +
25P GLN* 3.2 5.4 + - + +
26P GLN* 2.8 63.0 + - + +
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Residues in contact with LYS 23 (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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3D T 3.4 32.1 - - - +
4D T 4.4 6.4 + - - +
21P ASN* 2.8 12.5 + - - +
22P ILE* 1.3 76.3 - - + +
24P ALA* 1.3 63.9 + - - +
26P GLN* 3.2 12.1 + - - +
27P ALA* 2.9 23.6 + - - +
155P TYR 4.3 1.1 - - - +
156P PHE* 3.5 24.6 + - + +
157P SER* 4.8 1.8 - - - +
158P ASN* 3.2 36.8 + - - +
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Residues in contact with ALA 24 (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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18P PHE* 3.7 11.1 - - + -
19P ALA 3.2 26.0 - - - +
21P ASN* 2.9 21.0 + - - +
23P LYS* 1.3 71.3 - - - +
25P GLN* 1.3 64.2 + - - +
27P ALA* 3.0 14.2 + - - +
28P SER 3.1 10.0 + - - -
154P PRO 3.4 25.1 - - - +
155P TYR 3.9 1.1 - - - +
156P PHE* 3.7 15.3 - - + +
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Residues in contact with GLN 25 (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 GLN* 4.5 20.2 + - - +
18P PHE* 3.5 18.0 - - - +
19P ALA 3.3 18.8 - - - +
20P ASN* 4.6 6.9 - - - +
21P ASN 3.1 21.7 + - - +
22P ILE* 3.6 4.9 - - + +
24P ALA* 1.3 75.7 - - - +
26P GLN* 1.3 62.9 + - + +
28P SER* 2.6 26.9 + - - -
29P LYS* 3.1 43.7 + - - +
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Residues in contact with GLN 26 (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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3D T 5.1 6.1 + - - -
4D T 4.9 1.3 - - - +
22P ILE* 2.8 43.8 + - + +
23P LYS* 3.7 15.4 - - - +
25P GLN* 1.3 73.6 - - + +
27P ALA* 1.3 55.1 + - - +
29P LYS* 4.5 6.7 - - + +
30P ARG* 2.6 66.7 + - - +
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Residues in contact with ALA 27 (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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4D T 3.6 19.0 + - - +
23P LYS 2.9 12.1 + - - +
24P ALA 3.0 10.1 + - - +
26P GLN* 1.3 79.3 - - - +
28P SER* 1.3 62.1 + - - +
30P ARG* 3.6 9.1 + - - +
156P PHE* 3.7 30.3 - - + -
200P TYR* 2.7 33.8 + - + +
366P TYR* 4.6 1.2 - - - -
368P GLY* 5.6 1.9 - - - -
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Residues in contact with SER 28 (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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9P LEU* 3.3 13.3 - - - +
15P GLN* 5.4 0.7 + - - -
18P PHE* 3.4 48.4 - - - -
24P ALA 3.1 5.4 + - - -
25P GLN* 2.6 28.9 + - - -
27P ALA* 1.3 78.3 - - - +
29P LYS* 1.3 64.1 + - - +
30P ARG 4.7 0.3 - - - +
366P TYR* 2.7 22.8 + - - -
368P GLY* 5.6 0.7 - - - -
376P HIS* 3.1 12.0 + - - -
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Residues in contact with LYS 29 (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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9P LEU* 4.3 9.4 - - + -
25P GLN* 3.1 48.2 + - - +
26P GLN* 3.9 5.6 - - + +
28P SER* 1.3 84.3 + - - +
30P ARG* 1.3 67.6 + - - +
31P SER* 3.1 5.4 + - - -
376P HIS* 2.9 16.1 + - - -
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Residues in contact with ARG 30 (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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3D T 4.0 25.1 + - - -
4D T 3.7 37.2 + - + -
26P GLN* 2.6 53.9 + - - +
27P ALA* 3.7 12.6 - - - +
28P SER 3.5 0.9 - - - +
29P LYS* 1.3 68.5 - - - +
31P SER* 1.3 69.3 + - - +
33P LYS* 4.0 28.8 - - + +
200P TYR* 4.4 4.9 - - - +
368P GLY* 4.5 4.0 - - - +
369P ALA* 3.9 6.6 - - - +
376P HIS* 3.0 17.2 + - - -
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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