Contacts of the helix formed by residues 17 - 31 (chain A) in PDB entry 1HTI
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 ARG 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY* 1.3 103.5 + - - +
18A LYS* 1.3 67.0 + - - +
19A GLN* 3.3 6.3 - - + +
20A SER* 3.0 19.4 + - - +
21A LEU* 3.2 16.3 + - - +
47A TYR* 3.0 17.3 - - - +
70B THR* 2.9 35.3 + - - +
71B ASN* 2.6 36.8 + - - +
79B SER* 3.6 7.8 + - - -
81B GLY* 3.7 33.4 - - - -
82B MET* 3.5 6.5 - - - +
85B ASP* 3.9 11.9 - - - +
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Residues in contact with LYS 18 (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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17A ARG* 1.3 73.1 - - - +
19A GLN* 1.3 60.5 + - - +
22A GLY* 3.4 13.1 + - - -
47A TYR* 3.5 23.0 + - + -
50A PHE* 3.5 42.2 - - + -
54A LYS* 5.5 1.2 + - - -
49B ASP* 3.0 39.6 + - - -
53B GLN* 5.2 1.0 - - - +
85B ASP* 3.1 36.7 + - - +
86B CYS* 4.4 2.9 - - - -
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.1 6.3 + - + +
18A LYS* 1.3 76.8 - - - +
20A SER* 1.3 62.4 + - - +
22A GLY* 3.7 0.7 - - - -
23A GLU* 2.9 39.3 + - + +
85B ASP* 5.1 1.0 + - - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 4.3 4.8 - - - -
17A ARG* 3.0 30.8 + - - +
19A GLN* 1.3 77.4 + - - +
21A LEU* 1.3 58.0 + - - +
23A GLU* 3.1 14.3 + - - +
24A LEU* 2.8 28.8 + - - +
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Residues in contact with LEU 21 (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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12A TRP* 3.4 43.9 - - + -
15A ASN 3.7 18.2 - - - +
16A GLY* 4.1 8.7 - - - -
17A ARG 3.2 13.1 + - - +
20A SER* 1.3 75.6 - - - +
22A GLY* 1.3 61.3 + - - +
24A LEU* 3.1 8.6 + - + +
25A ILE* 2.9 33.3 + - - +
43A PRO* 5.0 0.2 - - + -
44A PRO* 4.7 3.4 - - + -
47A TYR* 3.8 38.1 - - + -
50A PHE* 4.0 13.9 - - + -
51A ALA* 5.5 0.7 - - + -
236A LEU* 4.2 15.5 - - + -
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Residues in contact with GLY 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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18A LYS 3.4 12.9 + - - -
19A GLN 3.4 5.9 + - - -
20A SER 3.3 0.2 - - - -
21A LEU* 1.3 77.8 - - - +
23A GLU* 1.3 60.8 + - - +
25A ILE* 3.2 9.5 + - - +
26A GLY* 3.0 19.9 + - - -
50A PHE* 3.8 13.3 - - - -
54A LYS* 4.8 9.3 - - - +
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Residues in contact with GLU 23 (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 GLN* 2.9 26.2 + - - +
20A SER* 3.1 12.6 + - - +
22A GLY* 1.3 74.2 - - - +
24A LEU* 1.3 62.3 + - - +
26A GLY* 3.1 11.7 + - - -
27A THR* 3.3 12.4 + - - -
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Residues in contact with LEU 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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12A TRP* 4.2 17.7 - - + -
20A SER 2.8 16.2 + - - +
21A LEU* 3.1 9.1 + - + +
23A GLU* 1.3 70.4 - - - +
25A ILE* 1.3 63.6 + - - +
26A GLY 3.0 1.0 + - - -
27A THR* 3.0 23.9 + - + +
28A LEU* 3.0 31.9 + - + +
235A SER 3.4 26.2 - - - +
236A LEU* 3.4 36.6 - - + +
237A LYS* 4.0 20.0 - - - +
238A PRO* 4.8 1.3 - - + -
240A PHE* 5.7 1.1 - - + -
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Residues in contact with ILE 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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12A TRP* 4.2 18.2 - - + -
21A LEU 2.9 23.7 + - - +
22A GLY* 3.2 14.8 + - - +
24A LEU* 1.3 70.9 - - - +
26A GLY* 1.3 63.4 + - - +
28A LEU* 3.2 9.9 + - - +
29A ASN* 3.0 30.1 + - - +
50A PHE* 3.9 19.1 - - + -
51A ALA* 4.1 17.5 - - + +
54A LYS* 3.4 43.7 - - + +
55A LEU* 3.3 26.9 - - + -
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Residues in contact with GLY 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 GLY 3.0 13.7 + - - -
23A GLU* 3.4 5.8 - - - -
24A LEU 3.0 0.6 - - - -
25A ILE* 1.3 75.1 - - - +
27A THR* 1.3 63.7 + - - +
29A ASN* 3.2 16.5 + - - +
30A ALA* 3.3 12.1 + - - +
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Residues in contact with THR 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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23A GLU 3.3 8.7 + - - -
24A LEU* 3.0 16.8 + - + -
26A GLY* 1.3 72.1 - - - +
28A LEU* 1.3 55.9 - - + +
30A ALA* 2.9 27.5 + - - +
31A ALA* 2.9 15.5 + - - +
238A PRO* 4.0 34.9 - - + +
241A VAL* 4.4 11.4 - - + -
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Residues in contact with LEU 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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12A TRP* 4.1 16.6 - - + +
24A LEU* 3.0 23.3 + - + +
25A ILE* 3.2 11.2 - - - +
27A THR* 1.3 82.3 - - + +
29A ASN* 1.3 57.7 + - - +
31A ALA* 3.4 19.8 - - - +
41A CYS* 3.9 24.9 - - - -
55A LEU* 4.1 14.1 - - + -
58A LYS* 4.4 2.4 - - - -
59A ILE* 3.2 30.6 - - + +
235A SER 5.7 0.2 - - - +
240A PHE* 3.5 31.9 - - + -
241A VAL* 4.8 8.3 - - + -
244A ILE* 4.4 9.0 - - + -
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Residues in contact with ASN 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 ILE* 3.0 18.3 + - - +
26A GLY* 3.5 8.4 - - - +
27A THR 3.1 0.2 - - - -
28A LEU* 1.3 74.6 - - - +
30A ALA* 1.3 56.0 + - - +
31A ALA 3.2 10.2 - - - +
54A LYS 3.2 23.8 + - - -
55A LEU* 3.3 15.2 - - - +
56A ASP* 3.0 44.4 + - + +
58A LYS* 4.5 7.6 + - - +
59A ILE* 4.6 0.9 - - - +
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Residues in contact with ALA 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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26A GLY 3.3 7.3 + - - +
27A THR* 2.9 9.6 + - - +
29A ASN* 1.3 75.3 - - - +
31A ALA* 1.3 66.4 + - - +
32A LYS* 4.0 2.3 + - - +
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Residues in contact with ALA 31 (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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27A THR 2.9 10.9 + - - +
28A LEU* 3.4 19.5 - - + +
29A ASN 3.8 2.4 - - - +
30A ALA* 1.3 83.9 - - - +
32A LYS* 1.3 53.7 + - - +
33A VAL* 6.4 0.4 - - + -
58A LYS* 2.4 28.2 + - - -
241A VAL* 3.7 35.0 - - + -
244A ILE* 5.8 3.8 - - + -
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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