Contacts of the strand formed by residues 43 - 46 (chain D) in PDB entry 3B4V
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 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D CYS* 3.7 11.1 - - - -
13D TRP 3.4 11.0 + - - -
14D LEU* 4.7 0.4 - - - +
15D GLN* 3.9 5.1 + - - -
26D LEU* 4.0 9.1 - - - +
35D CYS* 3.7 16.8 + - - +
36D CYS* 4.9 1.1 - - - -
38D SER* 4.4 4.9 - - - +
40D ASN* 3.3 38.8 - - + +
41D ILE 3.6 2.4 - - - +
42D ASP* 1.3 79.7 - - - +
44D ALA* 1.3 65.4 + - - +
69D CYS* 3.0 40.5 + - + +
70D LYS* 4.7 1.6 + - - +
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Residues in contact with ALA 44 (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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13D TRP* 2.7 35.6 + - - +
15D GLN* 3.8 16.4 - - + +
22D CYS* 3.6 29.6 - - - -
35D CYS* 3.2 9.6 - - - -
43D THR* 1.3 77.3 + - - +
45D TRP* 1.3 60.1 + - - +
66D CYS* 3.8 3.1 - - + -
67D LEU 3.4 16.4 - - - +
69D CYS* 4.0 3.3 - - - +
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Residues in contact with TRP 45 (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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8D PRO* 4.0 25.8 - - + -
10D GLY* 3.5 25.9 - - - -
11D VAL 3.3 21.7 + - - -
13D TRP* 4.4 1.8 - - - -
30D VAL* 2.8 22.8 + - + -
32D ARG* 3.3 51.3 - - + +
35D CYS* 3.6 27.6 - - + -
36D CYS* 4.8 2.2 - - - -
44D ALA* 1.3 76.2 - - - +
46D SER* 1.3 84.8 + - - +
47D ASN* 4.3 19.3 - - + -
65D HIS 4.0 0.3 - - - +
66D CYS* 3.8 2.5 - - - -
67D LEU* 2.9 40.3 + - + +
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Residues in contact with SER 46 (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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10D GLY* 3.5 6.9 - - - -
11D VAL* 2.9 29.9 + - - -
13D TRP* 3.1 29.1 - - - -
45D TRP* 1.3 87.4 - - - +
47D ASN* 1.3 63.7 + - - +
48D LEU* 3.6 12.3 + - - +
55D ILE* 5.7 0.2 - - - +
58D LEU* 5.6 2.1 - - - +
64D VAL* 3.6 10.3 - - - +
65D HIS* 2.9 22.7 + - - +
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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