Contacts of the strand formed by residues 42 - 46 (chain L) in PDB entry 6O81
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 GLU 42 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250E ARG* 5.9 1.7 + - - +
24L ARG* 5.2 6.4 - - - +
25L SER* 4.9 0.9 + - - -
32L TYR* 3.4 38.2 - - + +
33L VAL 3.4 14.8 - - - +
34L SER* 4.9 5.4 - - - -
35L LEU* 4.5 1.3 - - - -
40L ASN 3.9 2.1 + - - +
41L ILE* 1.3 74.2 - - - +
43L GLY* 1.3 65.2 + - - +
80L GLY 4.8 6.8 - - - +
82L ILE* 3.8 16.3 + - - +
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Residues in contact with GLY 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 5.8 2.5 - - - -
32L TYR* 3.4 7.2 - - - -
33L VAL* 2.9 41.9 + - - +
35L LEU* 4.0 11.3 - - - +
41L ILE 3.6 2.4 + - - -
42L GLU* 1.3 79.1 - - - +
44L MET* 1.3 61.9 + - - +
82L ILE* 3.8 13.9 - - - -
84L LEU* 4.7 0.4 - - - -
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Residues in contact with MET 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 3.6 33.4 - - - +
27L ALA* 5.0 0.4 - - + -
29L MET* 4.2 18.8 - - + +
30L GLY 4.0 29.8 - - - +
31L ALA 3.3 4.9 - - - +
32L TYR* 3.6 46.2 - - + -
33L VAL* 4.0 1.0 - - - +
43L GLY* 1.3 75.2 - - - +
45L ILE* 1.3 69.7 + - - +
46L LEU* 3.8 14.1 + - + +
82L ILE 3.1 9.9 + - - +
83L ASP* 3.6 2.3 - - - -
84L LEU* 2.8 33.4 + - - +
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Residues in contact with ILE 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 4.2 8.5 - - + -
23L VAL* 5.0 7.4 - - + -
30L GLY* 3.3 1.6 - - - -
31L ALA* 2.9 39.6 + - + +
33L VAL* 3.8 26.2 - - + -
44L MET* 1.3 72.3 - - - +
46L LEU* 1.3 73.4 + - - +
49L GLU 4.8 0.9 - - - +
50L LEU* 4.3 13.9 - - + +
68L GLU* 5.8 2.0 - - + -
70L VAL* 4.2 15.5 - - + -
84L LEU* 3.5 25.4 - - + +
85L SER* 4.3 0.7 - - - -
86L LYS* 4.1 37.7 - - + +
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Residues in contact with LEU 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 5.6 2.2 - - - +
29L MET 4.2 6.3 - - - +
30L GLY* 4.5 0.2 - - - -
44L MET* 4.0 26.5 - - + +
45L ILE* 1.3 76.4 - - - +
47L LEU* 1.3 65.6 + - - +
48L SER* 3.3 8.5 - - - +
49L GLU* 3.3 33.5 + - + +
50L LEU* 3.3 16.5 + - - +
73L ILE* 5.9 4.3 - - + -
83L ASP* 4.7 19.5 - - + -
84L LEU 3.3 13.9 + - - +
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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