Contacts of the helix formed by residues 21 - 30 (chain A) in PDB entry 1HNY
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 TRP 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP 4.0 4.9 - - - -
20A ARG* 1.3 71.6 - - - +
22A VAL* 1.3 56.9 + - - +
24A ILE* 3.1 7.8 + - + -
25A ALA* 2.9 29.5 + - - +
42A VAL* 3.7 26.0 - - + -
43A SER 3.5 24.0 - - - -
45A PRO* 3.7 31.1 + - + -
61A ARG* 3.9 2.5 - - - -
69A LEU 5.6 0.8 + - - -
71A THR* 3.8 4.9 + - - -
73A SER* 3.0 35.8 + - - +
74A GLY* 3.5 38.7 + - - +
75A ASN 3.8 0.8 + - - -
78A GLU* 3.7 21.5 - - + +
79A PHE* 3.6 36.3 - + - +
82A MET* 3.6 27.3 - - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.8 39.0 - - + +
21A TRP* 1.3 78.1 - - - +
23A ASP* 1.3 65.0 + - - +
25A ALA* 3.4 7.1 + - - +
26A LEU* 3.2 35.0 + - + +
73A SER 4.9 0.9 + - - +
78A GLU* 4.8 20.7 + - + +
81A ASN* 5.8 2.0 - - - +
85A ARG* 4.9 10.8 - - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.8 19.6 - - + -
20A ARG* 2.7 53.7 + - + +
22A VAL* 1.3 76.1 - - - +
24A ILE* 1.3 61.4 - - - +
26A LEU* 3.5 15.4 + - - +
27A GLU* 2.9 28.9 + - - +
30A ARG* 4.0 5.0 + - - +
368A LYS 4.5 0.3 - - - +
369A GLU* 4.4 4.2 - - - +
370A VAL* 3.3 37.2 + - + +
382A TRP* 5.8 0.3 - - - -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.1 18.6 - - + +
19A TRP* 3.9 26.0 - - + +
20A ARG 3.0 18.9 + - - +
21A TRP* 3.1 10.0 + - + +
23A ASP* 1.3 74.9 - - - +
25A ALA* 1.3 54.9 + - - +
27A GLU* 3.1 7.0 + - - +
28A CYS* 2.8 37.2 + - - -
40A VAL* 4.1 22.9 - - + -
42A VAL* 3.6 26.2 - - + -
43A SER 5.9 0.2 - - - +
82A MET* 3.6 27.8 - - + -
86A CYS* 4.2 9.6 - - - -
93A ILE* 4.2 3.6 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TRP 2.9 14.6 + - - +
22A VAL* 3.6 5.6 - - - +
23A ASP 3.3 0.2 - - - -
24A ILE* 1.3 77.6 - - - +
26A LEU* 1.3 63.0 + - - +
28A CYS* 3.3 10.2 + - - +
29A GLU* 3.4 18.7 + - - +
81A ASN* 4.4 2.2 - - - +
82A MET* 3.9 19.7 - - + +
85A ARG* 3.5 35.7 - - + +
86A CYS* 4.2 11.7 - - - -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.2 26.6 + - + +
23A ASP* 3.7 15.7 - - - +
25A ALA* 1.3 76.1 - - - +
27A GLU* 1.3 60.3 + - - +
29A GLU* 3.2 9.2 + - - +
30A ARG* 2.9 59.9 + - + +
85A ARG* 3.7 20.0 - - - +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.4 3.4 - - + -
19A TRP* 3.9 23.3 - - + -
23A ASP 2.9 18.7 + - - +
24A ILE* 3.5 5.6 - - - +
26A LEU* 1.3 75.8 - - - +
28A CYS* 1.3 65.0 + - - +
30A ARG* 2.9 25.0 + - - +
31A TYR* 3.0 15.2 + - - +
32A LEU* 2.9 37.4 + - + -
372A ILE* 4.4 0.2 - - - +
386A HIS* 2.6 32.8 + - - +
387A ARG* 2.8 39.4 + - - -
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Residues in contact with CYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 2.8 19.7 + - - -
25A ALA 3.5 6.1 - - - +
26A LEU 3.2 0.2 - - - -
27A GLU* 1.3 73.3 - - - +
29A GLU* 1.3 61.7 + - + +
32A LEU* 3.8 14.8 - - - -
33A ALA* 2.9 33.2 + - - +
40A VAL* 4.7 1.3 - - - -
85A ARG 5.0 0.4 - - - +
86A CYS* 2.1 59.0 - - - +
89A VAL* 5.2 1.8 - - + -
91A VAL* 3.8 22.0 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.6 8.9 - - - +
26A LEU* 3.2 9.9 + - + +
28A CYS* 1.3 80.1 - - + +
30A ARG* 1.3 60.0 + - + +
33A ALA* 4.8 1.3 - - - +
34A PRO* 3.7 12.8 - - - +
85A ARG* 2.9 60.9 + - - +
89A VAL* 4.0 26.1 - - + +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP* 4.5 1.2 - - - -
23A ASP* 4.0 17.8 + - - +
26A LEU* 2.9 57.5 + - + +
27A GLU* 2.9 29.0 + - - +
29A GLU* 1.3 75.7 - - + +
31A TYR* 1.3 63.5 + - - +
34A PRO* 3.7 10.3 - - - +
370A VAL* 4.5 21.2 + - - +
372A ILE* 4.0 26.6 - - - +
387A ARG* 3.6 11.2 + - - +
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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