Contacts of the strand formed by residues 42 - 45 (chain O) in PDB entry 6T9L
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 ARG 42 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237K ASP* 4.3 4.7 + - - -
239K HIS* 3.2 26.4 + - - -
240K GLU* 3.5 44.5 - - - +
243K GLN* 4.0 7.3 + - - +
361K GLN* 4.9 0.8 - - - +
40O GLN 4.2 1.1 - - - +
41O GLN* 1.3 76.3 - - - +
43O LEU* 1.3 61.6 + - - +
44O ILE* 3.4 22.5 - - + +
49O GLN* 4.1 13.8 + - - +
68O HIS 3.2 6.6 - - - +
69O LEU* 3.7 2.4 - - - +
70O VAL* 2.9 61.8 + - + +
71O LEU 4.1 11.1 + - - -
72O ARG* 3.6 46.2 - - + +
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Residues in contact with LEU 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O VAL* 5.9 3.8 - - + -
23O ILE* 5.6 2.5 - - + -
26O VAL* 4.3 21.3 - - + -
27O LYS* 4.5 22.4 - - + +
30O ILE* 5.9 2.7 - - + -
41O GLN* 4.1 24.4 + - + +
42O ARG* 1.3 74.8 - - - +
44O ILE* 1.3 65.1 + - - +
49O GLN* 3.5 2.7 - - - +
50O LEU* 3.1 60.2 + - + +
67O LEU* 4.1 24.9 - - + -
68O HIS 3.6 6.7 - - - +
69O LEU* 4.6 8.7 - - + -
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Residues in contact with ILE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K HIS* 4.7 2.7 - - + -
243K GLN* 3.4 41.7 - - - +
305K ASP* 4.5 4.5 - - - +
42O ARG* 3.4 24.5 - - - +
43O LEU* 1.3 82.0 - - - +
45O PHE* 1.3 65.5 + - - +
47O GLY* 4.1 13.9 - - - +
48O LYS 3.7 3.4 - - - +
49O GLN* 3.9 15.0 - - + -
67O LEU* 4.2 2.4 - - - +
68O HIS* 3.2 46.7 + - + +
70O VAL* 4.1 22.9 - - + -
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Residues in contact with PHE 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K ASP* 4.7 24.0 - - + -
302K PRO* 5.7 3.6 - - + -
43O LEU 4.2 0.2 - - - -
44O ILE* 1.3 75.8 - - - +
46O ALA* 1.3 84.0 + - + +
47O GLY 3.1 0.9 - - - -
48O LYS* 3.0 27.0 + - - +
50O LEU* 4.5 13.6 - - + +
59O TYR* 4.2 15.5 - + + -
60O ASN* 4.6 4.3 - - + -
61O ILE* 4.0 34.1 - - + -
62O GLN 5.5 0.4 - - - -
65O SER* 3.1 26.2 - - - -
66O THR 3.5 20.6 - - - -
67O LEU* 3.9 15.5 - - + -
68O HIS* 5.1 3.4 - + - -
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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