Contacts of the strand formed by residues 18 - 24 (chain H) in PDB entry 1BHC
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 ILE 18 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17G ARG 4.7 5.4 - - - +
19G ILE* 3.4 32.3 - - + +
16H ALA* 3.1 36.6 - - + -
17H ARG* 1.3 78.2 - - - +
19H ILE* 1.3 76.9 + - - +
20H ARG* 3.8 22.9 - - - +
34H VAL* 3.5 2.1 - - - -
35H TYR* 2.7 47.3 + - + +
37H GLY* 4.8 0.4 - - - -
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Residues in contact with ILE 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ARG 4.2 0.4 + - - -
18H ILE* 1.3 80.9 - - - +
20H ARG* 1.3 74.7 + - - +
21H TYR* 4.7 13.7 - - + +
32H THR* 3.8 26.0 - - + -
33H PHE 3.5 3.8 - - - +
34H VAL* 5.2 0.9 - - + -
46H LYS 5.2 1.7 - - - +
16I ALA* 5.0 1.6 - - + -
18I ILE* 3.4 41.9 - - + +
20I ARG* 4.1 21.5 - - - +
35I TYR* 4.1 9.6 - - + -
37I GLY* 3.9 24.5 - - - +
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Residues in contact with ARG 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU* 2.4 46.6 + - - -
53E ARG* 3.8 7.1 - - - +
19G ILE* 4.2 10.3 - - - +
21G TYR* 5.2 0.6 + - - -
32G THR* 4.5 2.6 - - - +
18H ILE* 3.8 17.2 - - + +
19H ILE* 1.3 83.7 + - - +
21H TYR* 1.3 67.0 + - - +
32H THR* 3.2 6.1 - - - -
33H PHE* 2.9 45.2 + - + +
35H TYR* 3.4 39.5 - - + -
44H ASN* 3.1 24.6 + - - +
45H PHE 3.6 7.4 - - - +
46H LYS* 3.8 27.4 - - - +
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Residues in contact with TYR 21 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49D GLU* 2.7 35.8 + - + +
52D MET* 5.6 2.0 - - + -
19H ILE* 4.7 10.7 - - + +
20H ARG* 1.3 77.7 - - - +
22H PHE* 1.3 62.5 + - - +
30H CYS* 4.6 5.2 - - + -
31H GLN* 3.1 18.4 - - - +
32H THR* 3.5 23.3 - - + +
33H PHE* 3.6 2.2 - - - -
44H ASN* 3.5 6.2 - - - -
45H PHE* 2.8 43.5 + - - +
46H LYS 3.9 12.1 - - - -
48H ALA* 3.7 41.3 - - + -
51H CYS* 4.1 21.3 - - + -
20I ARG* 5.3 0.5 + - - -
46I LYS* 4.2 17.2 + - - +
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Residues in contact with PHE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU 4.9 0.2 - - - -
8H PRO* 5.4 0.7 - - + -
9H PRO* 3.5 36.8 - - + -
21H TYR* 1.3 74.7 - - - +
23H TYR* 1.3 68.0 + - - +
24H ASN* 3.5 22.6 + - + -
30H CYS* 3.1 2.3 - - - -
31H GLN* 2.8 75.1 + - + -
32H THR 3.4 19.7 - - - -
33H PHE* 3.6 25.4 - + + -
43H ASN* 3.5 27.1 - - - +
51H CYS* 3.6 7.0 - - - -
39I ARG* 5.3 10.3 - - - -
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Residues in contact with TYR 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H ARG* 3.1 39.2 + - - -
5H CYS* 3.4 31.3 - - + +
6H LEU* 5.5 0.2 - - - -
7H GLU 4.4 2.1 - - - +
22H PHE* 1.3 75.5 - - - +
24H ASN* 1.3 57.8 + - - +
25H ALA* 3.4 22.5 + - + -
28H GLY* 3.2 25.0 + - - -
29H LEU* 3.6 24.5 - - - -
30H CYS* 3.8 15.7 - - - -
43H ASN* 2.9 28.8 + - - +
51H CYS* 3.6 2.0 - - - -
55H CYS* 3.4 37.5 - - + -
56H GLY* 4.1 10.5 - - - -
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Residues in contact with ASN 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H PHE* 3.5 20.5 + - + -
23H TYR* 1.3 72.1 - - - +
25H ALA* 1.3 51.0 + - - +
26H LYS* 3.1 22.3 + - - +
27H ALA* 3.1 15.7 + - + +
28H GLY 2.6 32.4 + - - -
29H LEU 2.7 20.7 + - - +
31H GLN* 2.8 33.9 + - + +
39I ARG* 6.0 1.0 - - - +
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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