Contacts of the strand formed by residues 49 - 53 (chain D) in PDB entry 1JLH
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 HIS 49 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C PHE* 3.8 24.9 - - + -
550C GLN* 5.0 4.5 + - - -
551C GLN* 3.7 28.1 + - - +
42D THR* 5.5 5.8 - - - -
43D LEU 3.1 9.4 + - - +
44D ASN* 3.3 47.3 + - + +
48D GLY* 1.3 75.9 - - - -
50D ILE* 1.3 62.5 + - - +
477D VAL 3.9 0.3 - - - +
478D PHE* 3.2 6.4 - - - +
479D THR* 2.8 30.7 + - - -
485D MET* 3.9 0.2 - - - +
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C PHE* 4.5 1.8 - - - -
41D LEU 3.6 3.1 - - - +
42D THR* 3.6 0.6 - - - -
43D LEU* 2.8 49.8 + - + +
45D THR* 4.1 19.3 - - + -
49D HIS* 1.3 73.7 - - - +
51D LEU* 1.3 61.8 + - - +
52D VAL* 3.9 20.6 + - + -
302D MET* 4.1 24.0 - - + -
476D ILE* 4.3 16.8 - - + -
477D VAL 3.5 3.6 - - - +
478D PHE* 4.4 2.2 - - + +
485D MET* 3.5 36.8 - - + -
488D ALA* 4.2 6.3 - - + -
489D LEU* 4.6 10.3 - - + -
492D MET* 5.2 3.6 - - - -
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Residues in contact with LEU 51 (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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544C LEU* 3.9 24.9 - - + -
547C PHE* 3.5 53.3 - - + -
36D PHE* 4.1 18.4 - - + -
40D SER* 4.1 20.9 - - - -
41D LEU 3.3 15.5 - - - +
42D THR* 3.8 16.2 - - + +
50D ILE* 1.3 71.6 - - - +
52D VAL* 1.3 60.8 + - - +
53D ASP* 4.3 5.8 - - + +
475D SER 3.2 7.3 - - - +
476D ILE* 3.4 1.4 - - - -
477D VAL* 2.7 34.2 + - + +
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Residues in contact with VAL 52 (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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40D SER* 3.3 3.6 - - - -
41D LEU* 2.8 48.3 + - + +
43D LEU* 5.0 3.4 - - + -
50D ILE* 4.0 20.0 - - + +
51D LEU* 1.3 74.1 - - - +
53D ASP* 1.3 60.1 + - - +
54D TYR* 3.6 14.9 + - + -
315D ALA* 4.4 11.7 - - + +
318D LEU* 6.4 1.3 - - + -
319D LEU* 4.3 20.4 - - + -
474D ASN* 5.8 0.2 - - - +
476D ILE* 3.4 28.0 - - + -
492D MET* 4.4 15.0 - - - -
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Residues in contact with ASP 53 (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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540C SER* 2.7 22.8 + - - -
544C LEU* 3.5 23.6 - - + +
36D PHE* 3.3 28.1 - - + -
39D PHE 3.7 1.7 - - - +
40D SER* 4.0 5.4 - - - -
51D LEU* 3.6 3.5 + - + -
52D VAL* 1.3 71.6 - - - +
54D TYR* 1.3 58.8 + - - +
55D SER* 2.5 31.3 + - - -
56D LYS* 5.1 1.9 + - - +
473D THR 4.4 1.0 - - - +
474D ASN* 3.5 4.3 - - - -
475D SER* 2.9 42.5 + - - +
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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