Contacts of the strand formed by residues 18 - 24 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ARG 4.6 5.6 - - - +
19C ILE* 3.5 31.2 - - + +
16D ALA* 3.1 36.3 - - + -
17D ARG* 1.3 76.4 - - - +
19D ILE* 1.3 78.4 + - - +
20D ARG* 3.8 25.8 - - + +
34D VAL* 3.4 3.5 - - - -
35D TYR* 2.6 45.7 + - + +
37D GLY* 4.8 0.4 - - - -
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Residues in contact with ILE 19 (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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17D ARG 4.2 0.6 + - - -
18D ILE* 1.3 78.2 - - - +
20D ARG* 1.3 76.9 + - - +
21D TYR* 4.7 13.0 - - + +
32D THR* 3.9 24.5 - - + -
33D PHE 3.5 5.2 - - - +
34D VAL* 5.2 0.9 - - + -
46D LYS* 5.2 2.1 - - - +
16E ALA* 5.0 1.3 - - + -
18E ILE* 3.4 41.4 - - + +
20E ARG* 4.2 13.5 - - - +
35E TYR* 4.0 18.2 - - + -
37E GLY* 3.9 24.0 - - - +
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Residues in contact with ARG 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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19C ILE* 4.2 8.9 - - - +
21C TYR* 4.7 1.4 + - - -
32C THR* 4.5 2.2 - - - +
18D ILE* 3.8 17.0 - - + +
19D ILE* 1.3 83.3 - - - +
21D TYR* 1.3 66.1 + - - +
32D THR* 3.1 7.4 - - - -
33D PHE* 2.9 49.0 + - + -
35D TYR* 3.4 39.7 - - + -
44D ASN* 3.2 18.9 + - - +
45D PHE 3.6 8.1 - - - -
46D LYS* 3.7 27.4 - - - +
49I GLU* 2.4 46.6 + - - -
53I ARG* 3.8 6.7 - - - +
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Residues in contact with TYR 21 (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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19D ILE* 4.7 9.6 - - + +
20D ARG* 1.3 78.0 - - - +
22D PHE* 1.3 62.3 + - - +
30D CYS* 4.6 4.9 - - + -
31D GLN* 3.0 15.7 - - - +
32D THR* 3.5 26.4 - - + +
33D PHE* 3.6 2.4 - - - -
44D ASN* 3.5 6.2 - - - -
45D PHE* 2.8 45.2 + - - +
46D LYS 3.8 11.4 - - - -
48D ALA* 3.6 41.5 - - + +
51D CYS* 4.2 20.9 - - + -
20E ARG* 5.2 0.5 + - - -
46E LYS* 4.2 16.1 + - - +
49H GLU* 2.7 35.3 + - + +
52H MET* 5.7 1.3 - - - -
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Residues in contact with PHE 22 (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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7D GLU 5.0 0.4 - - - -
8D PRO* 5.5 0.2 - - + -
9D PRO* 3.7 34.5 - - + -
21D TYR* 1.3 75.5 - - - +
23D TYR* 1.3 68.7 + - - +
24D ASN* 3.5 24.4 + - + -
30D CYS* 3.1 1.4 - - - -
31D GLN* 2.8 72.7 + - + -
32D THR 3.4 19.7 - - - -
33D PHE* 3.6 26.0 - + + -
43D ASN* 3.4 27.8 - - - +
45D PHE* 4.6 0.2 - - - -
51D CYS* 3.6 7.0 - - - -
39E ARG* 5.2 10.3 - - - -
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Residues in contact with TYR 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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1D ARG* 3.2 40.5 + - - -
5D CYS* 3.4 28.2 - - + +
6D LEU 5.6 0.2 - - - -
7D GLU 4.4 1.6 - - - +
22D PHE* 1.3 74.4 - - - +
24D ASN* 1.3 58.7 + - - +
25D ALA* 3.4 24.3 + - + -
28D GLY* 3.3 24.1 + - - -
29D LEU* 3.6 24.9 - - - -
30D CYS* 3.9 11.4 - - - -
43D ASN* 2.8 28.2 + - - +
51D CYS* 3.7 5.1 - - - -
55D CYS* 3.4 38.4 - - + -
56D GLY* 4.0 11.4 - - - -
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Residues in contact with ASN 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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22D PHE* 3.5 20.5 + - + -
23D TYR* 1.3 72.5 - - - +
25D ALA* 1.3 50.1 + - - +
26D LYS* 3.0 23.9 + - - +
27D ALA* 3.1 15.8 + - + +
28D GLY* 2.6 33.1 + - - -
29D LEU 2.7 20.6 + - - +
31D GLN* 2.8 33.4 + - + +
39E ARG* 6.0 1.6 - - - +
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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