Contacts of the strand formed by residues 39 - 43 (chain R) in PDB entry 3ALQ
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 GLN 39 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35R CYS* 3.8 3.2 - - + +
36R SER* 2.9 53.7 + - - +
38R GLY* 1.3 81.2 - - - +
40R HIS* 1.3 58.1 + - - +
53R CYS* 3.2 28.3 - - - +
54R ASP* 3.0 26.2 - - - +
55R SER* 4.0 5.6 + - - +
56R CYS* 4.1 2.2 - - - +
62R THR* 3.1 6.5 + - - -
66R ASN* 3.0 24.3 + - - -
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Residues in contact with HIS 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2R CO 2.3 31.4 + - - -
35R CYS* 3.4 6.2 - - - -
39R GLN* 1.3 74.5 - - - +
41R ALA* 1.3 73.6 + - - +
42R LYS* 3.8 17.9 - - + -
53R CYS* 3.3 3.8 - - - -
54R ASP* 2.8 54.6 + - + -
55R SER 4.0 3.4 - - - -
57R GLU* 5.2 1.1 - - - -
62R THR* 4.8 0.2 - - + -
66R ASN* 3.9 6.1 - - - +
68R VAL* 3.5 12.3 - - + +
69R PRO 2.8 24.9 + - - -
70R GLU* 3.9 21.9 + - - +
71R CYS* 3.6 28.0 - - - -
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Residues in contact with ALA 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R CYS* 3.5 17.3 - - - -
40R HIS* 1.3 80.4 + - - +
42R LYS* 1.3 60.5 + - - +
43R VAL 4.8 1.3 - - - +
44R PHE* 4.0 21.7 - - + -
51R THR* 4.3 10.5 - - + -
52R VAL 4.0 1.1 - - - -
66R ASN* 4.1 1.6 + - - -
67R TRP* 3.9 20.2 - - - +
68R VAL 2.7 18.8 + - - +
69R PRO* 3.1 15.4 - - - +
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Residues in contact with LYS 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R HIS* 3.4 12.6 + - + -
41R ALA* 1.3 75.2 - - - +
43R VAL* 1.3 73.9 + - + +
44R PHE* 5.8 1.7 - - - -
52R VAL* 2.8 23.5 + - + +
54R ASP* 3.8 31.4 - - + +
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Residues in contact with VAL 43 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R ALA 5.1 0.4 - - - -
42R LYS* 1.3 100.4 - - + +
44R PHE* 1.3 75.3 + - - +
46R THR* 6.4 0.2 - - + -
49R SER* 5.9 2.5 - - - +
50R ASP 5.7 0.2 - - - +
51R THR* 3.6 6.2 - - - +
52R VAL* 2.8 58.5 + - + +
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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