Contacts of the helix formed by residues 19 - 30 (chain D) in PDB entry 4HFX
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 THR 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.9 9.7 - - + +
64A TYR* 3.8 23.3 - - - +
68A GLN* 3.7 9.0 + - - +
71A ARG* 5.1 3.6 - - - +
17D ARG 5.0 3.1 - - - +
18D CYS* 1.3 77.8 - - - +
20D PRO* 1.4 66.9 - - + +
21D ASP* 3.3 18.2 + - - -
22D GLN* 2.9 19.9 + - - +
23D LEU* 2.7 33.2 + - - +
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Residues in contact with PRO 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 4.7 15.0 - - + -
18D CYS 4.2 0.6 - - - +
19D THR* 1.4 86.7 - - + +
21D ASP* 1.3 57.0 + - - +
23D LEU* 3.3 9.4 + - + +
24D TYR* 2.8 30.6 + - - +
64D TYR* 3.0 48.9 - - + +
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Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 3.2 22.5 - - + +
20A PRO* 3.9 6.6 - - - +
21A ASP* 2.9 41.8 + - - +
68A GLN* 4.8 3.3 + - - -
19D THR* 3.3 14.6 + - - -
20D PRO* 1.3 77.9 - - - +
22D GLN* 1.3 64.1 + - - +
24D TYR* 3.8 9.1 - - - +
25D ARG* 2.8 58.3 + - - +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 3.0 59.1 + - - +
71A ARG* 3.4 34.3 + - - +
72A GLU* 4.1 9.3 - - + +
75A LEU* 4.6 10.5 - - + -
18D CYS* 4.0 4.2 - - + -
19D THR* 2.9 23.8 + - - +
21D ASP* 1.3 83.2 + - - +
23D LEU* 1.3 64.4 + - - +
25D ARG* 3.4 20.4 + - - +
26D ILE* 3.0 29.9 + - + +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 4.0 43.3 - - + +
18D CYS* 4.1 10.4 - - + +
19D THR 2.7 16.7 + - - +
20D PRO* 3.5 12.1 - - + +
22D GLN* 1.3 72.1 - - - +
24D TYR* 1.3 50.6 - - - +
26D ILE* 3.2 10.2 + - + +
27D GLU* 2.8 62.1 + - + +
36D GLU* 4.8 16.2 - - + +
38D ASP 5.7 1.6 - - - +
39D GLN* 5.2 11.2 - - + -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 5.6 6.1 + - - -
20D PRO 2.8 20.2 + - - +
21D ASP* 3.8 9.2 - - - +
23D LEU* 1.3 74.2 - - - +
25D ARG* 1.3 56.1 + - + +
27D GLU* 3.2 18.8 + - - +
28D GLU* 2.8 76.9 + - + +
65D LEU* 3.8 40.4 - - + -
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASP* 4.2 16.4 - - - +
68A GLN* 4.3 11.7 - - - +
72A GLU* 2.7 33.8 + - + +
21D ASP* 2.8 52.6 + - - +
22D GLN* 3.6 29.8 - - + +
23D LEU 3.3 0.2 - - - -
24D TYR* 1.3 76.6 - - + +
26D ILE* 1.3 62.6 + - + +
28D GLU* 3.3 7.4 + - - +
29D TYR* 2.9 28.5 + - - +
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Residues in contact with ILE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLU* 4.6 14.1 - - + +
75A LEU* 3.4 46.0 - - + -
76A ARG* 4.5 4.7 - - + +
79A THR* 4.0 21.3 - - + +
15D LEU* 5.0 7.2 - - + -
18D CYS* 5.1 2.2 - - - -
22D GLN* 3.0 21.4 + - + +
23D LEU* 3.5 11.4 - - + +
25D ARG* 1.3 77.5 - - + +
27D GLU* 1.3 58.0 + - + +
29D TYR* 3.2 8.3 + - + +
30D ASN* 2.9 27.7 + - - +
33D LEU* 3.6 25.6 - - + -
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 2.8 34.3 + - + +
24D TYR* 3.2 26.6 + - - +
26D ILE* 1.3 77.5 - - - +
28D GLU* 1.3 63.2 + - - +
30D ASN 3.0 27.3 - - - +
31D HIS* 3.2 12.0 - - - +
33D LEU* 4.4 25.2 - - + +
36D GLU* 3.1 29.5 - - + +
65D LEU* 5.9 1.2 - - - +
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 4.6 20.2 + - - +
24D TYR* 2.8 69.8 + - + +
25D ARG* 3.8 6.7 - - + +
27D GLU* 1.3 75.7 - - - +
29D TYR* 1.3 63.9 + - - +
31D HIS* 4.0 11.0 + - - -
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Residues in contact with TYR 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.3 72.6 + - + +
79A THR* 3.5 18.4 - - - -
80A LYS* 3.5 49.2 + - + +
25D ARG 2.9 16.2 + - - +
26D ILE* 3.2 11.9 + - + +
28D GLU* 1.3 79.4 - - - +
30D ASN* 1.3 62.1 + - + +
31D HIS* 4.1 8.4 + - - -
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 2.5 31.6 + - - +
80A LYS* 4.3 11.3 + - - +
81A ASN* 3.3 28.2 + - - +
26D ILE 2.9 11.3 + - - +
27D GLU 3.0 9.1 - - - +
29D TYR* 1.3 84.0 - - + +
31D HIS* 1.3 69.7 + - - +
32D VAL* 3.4 19.9 + - - +
33D LEU* 3.2 37.6 + - + +
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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