Contacts of the helix formed by residues 19 - 28 (chain D) in PDB entry 3CB4
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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13D ILE 4.1 24.2 - - - +
18D SER* 1.3 75.7 - - - +
20D LEU* 1.3 66.4 + - - +
21D SER* 3.9 9.4 - - - -
22D ASP* 2.9 38.0 + - - +
23D ARG* 3.2 10.9 + - - +
132D LYS* 5.5 2.0 - - - +
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Residues in contact with LEU 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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9D ILE* 5.3 5.4 - - + -
19D THR* 1.3 73.0 - - - +
21D SER* 1.3 62.9 + - - +
23D ARG* 3.2 32.5 + - - +
24D ILE* 3.0 38.8 + - + +
99D LEU* 4.1 21.3 - - + -
101D VAL* 3.5 39.2 - - + +
129D VAL* 4.2 11.7 - - + -
131D ASN* 4.1 3.4 + - - +
161D CYS* 3.9 20.0 - - - -
169D VAL* 4.0 18.6 - - + -
172D VAL* 4.4 6.3 - - + -
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Residues in contact with SER 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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9D ILE* 4.2 15.0 - - - +
19D THR* 3.9 12.5 - - - -
20D LEU* 1.3 79.8 - - - +
22D ASP* 1.3 67.9 + - - +
24D ILE* 3.5 4.9 + - - +
25D ILE* 3.3 27.9 + - - +
59D VAL* 5.4 0.5 - - - +
75D PHE* 3.4 32.3 - - - -
77D ASP* 5.7 5.6 + - - -
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Residues in contact with ASP 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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18D SER* 4.6 8.0 - - - -
19D THR* 2.9 28.0 + - - +
21D SER* 1.3 81.4 + - - +
23D ARG* 1.3 64.8 - - - +
25D ILE* 3.4 17.4 + - - +
26D GLN* 3.3 34.0 + - - +
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Residues in contact with ARG 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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18D SER* 2.7 54.6 + - - -
19D THR* 3.2 6.9 + - - +
20D LEU* 3.2 34.8 + - - +
22D ASP* 1.3 74.6 - - - +
24D ILE* 1.3 66.0 + - - +
26D GLN* 3.3 20.5 + - - +
27D ILE* 3.3 20.2 + - + +
131D ASN* 2.6 41.8 + - - +
132D LYS* 4.6 0.8 - - - +
161D CYS* 4.4 1.8 - - - -
162D SER 3.5 10.7 + - - -
163D ALA* 3.5 35.3 - - - +
166D GLY* 5.0 8.7 - - - -
169D VAL* 4.2 19.0 - - + +
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Residues in contact with ILE 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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7D PHE* 4.6 8.1 - - + -
9D ILE* 4.3 20.4 - - + -
20D LEU* 3.0 37.0 + - + +
21D SER* 3.7 5.8 - - - +
23D ARG* 1.3 77.4 - - - +
25D ILE* 1.3 62.9 + - - +
27D ILE* 3.1 17.9 + - - +
28D CYS* 3.2 11.5 + - - -
61D LEU* 3.9 17.9 - - + -
73D LEU* 5.3 3.4 - - + -
75D PHE* 4.8 8.3 - - + -
99D LEU* 4.4 10.3 - - + -
169D VAL* 4.1 16.4 - - + -
172D VAL* 5.3 1.3 - - + -
173D LEU* 3.7 35.2 - - + -
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Residues in contact with ILE 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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21D SER* 3.3 26.0 - - - +
22D ASP* 3.4 19.0 + - - +
23D ARG 3.3 0.2 - - - -
24D ILE* 1.3 76.1 - - - +
26D GLN* 1.3 61.6 + - + +
28D CYS 3.2 9.9 + - - -
29D GLY 3.7 0.5 + - - -
30D GLY 3.2 38.2 + - - +
59D VAL* 4.4 22.2 - - + -
61D LEU* 3.9 24.5 - - + -
75D PHE* 4.7 3.1 - - + -
242D PRO* 4.2 24.5 - - + -
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Residues in contact with GLN 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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18D SER* 5.2 6.1 + - - -
22D ASP* 3.3 28.1 + - - +
23D ARG* 3.6 18.1 - - - +
24D ILE 3.1 1.0 - - - -
25D ILE* 1.3 75.4 - - + +
27D ILE* 1.3 63.2 + - + +
28D CYS 3.1 12.6 + - - +
30D GLY* 4.5 16.7 - - - -
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Residues in contact with ILE 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 ARG* 3.3 11.9 + - + +
24D ILE* 3.1 15.4 + - - +
26D GLN* 1.3 78.7 - - + +
28D CYS* 1.3 60.0 + - - +
63D TYR* 5.0 7.4 - - + -
166D GLY* 5.2 6.7 - - - +
169D VAL* 3.7 17.9 - - + +
170D GLN* 3.6 43.3 - - + +
173D LEU* 3.6 23.3 - - + -
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Residues in contact with CYS 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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24D ILE* 3.2 11.9 + - - +
25D ILE 3.2 4.4 - - - +
26D GLN 3.1 8.2 - - - +
27D ILE* 1.3 84.9 - - - +
29D GLY* 1.3 73.8 + - - +
30D GLY* 2.9 2.8 + - - -
61D LEU* 3.8 26.5 - - + -
62D ASP 3.3 26.0 - - - +
63D TYR* 4.2 7.6 - - - -
73D LEU* 4.6 2.2 - - - -
173D LEU* 3.7 28.3 - - - -
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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