Contacts of the strand formed by residues 30 - 35 (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 GLY 30 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26L ILE* 3.9 2.6 - - - +
27L ALA* 2.9 32.4 + - - +
28L GLU 3.3 2.6 - - - -
29L MET* 1.3 79.9 - - - +
31L ALA* 1.3 59.9 + - - -
44L MET* 4.0 11.1 - - - +
45L ILE 3.3 11.9 - - - -
47L LEU* 4.0 13.0 - - - -
58L ILE* 5.7 4.3 - - - -
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Residues in contact with ALA 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L VAL* 4.1 13.9 - - + -
25L SER 3.6 5.4 - - - +
26L ILE* 3.7 21.5 - - + -
30L GLY* 1.3 72.3 - - - -
32L TYR* 1.3 63.6 + - - +
33L VAL* 3.4 4.9 + - + +
44L MET* 3.3 5.7 - - - +
45L ILE* 2.9 45.6 + - + +
50L LEU* 5.8 6.1 - - + -
58L ILE* 6.3 0.7 - - + -
62L ILE* 5.2 3.6 - - + -
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Residues in contact with TYR 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250E ARG* 4.4 30.7 - - + -
254E ASN* 4.8 15.0 - - - -
23L VAL* 3.9 0.9 - - - +
24L ARG* 2.9 23.6 + - + -
25L SER* 2.9 38.9 + - - +
27L ALA* 3.7 25.6 - - + -
31L ALA* 1.3 71.2 - - - +
33L VAL* 1.3 59.7 + - - +
42L GLU* 3.4 34.8 - - + +
43L GLY 3.4 6.1 - - - -
44L MET* 3.6 27.8 - - + -
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Residues in contact with VAL 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 3.9 15.7 - - + -
22L ASN 3.4 9.9 - - - +
23L VAL* 3.7 25.4 - - + +
24L ARG* 4.1 3.4 - - - +
31L ALA* 3.8 9.2 - - + +
32L TYR* 1.3 77.0 - - - +
34L SER* 1.3 60.7 + - - +
35L LEU* 4.7 0.4 - - + -
42L GLU* 3.4 13.3 - - - +
43L GLY* 2.9 46.9 + - - +
44L MET 4.0 0.7 - - - +
45L ILE* 3.8 24.7 - - + -
84L LEU* 3.7 23.8 - - + -
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Residues in contact with SER 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 3.4 5.3 - - - -
22L ASN* 2.4 63.5 + - - +
24L ARG* 5.3 5.9 - - - +
33L VAL* 1.3 76.3 - - - +
35L LEU* 1.3 62.9 + - - +
36L LEU 3.3 1.6 + - - -
40L ASN* 3.8 25.0 + - - -
41L ILE 3.5 6.7 - - - -
42L GLU* 4.9 6.3 - - - -
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Residues in contact with LEU 35 (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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13L PRO* 3.9 23.3 - - + -
19L VAL* 4.0 14.4 - - + -
20L MET 4.2 0.9 - - - +
21L VAL* 3.8 24.0 - - + -
33L VAL* 4.7 0.2 - - + -
34L SER* 1.3 70.2 - - - +
36L LEU* 1.3 62.7 + - - +
37L GLU* 3.2 1.3 - - + +
38L TYR* 3.2 33.0 + - + -
40L ASN* 3.0 23.8 + - - -
41L ILE* 2.9 38.7 + - + +
42L GLU 4.5 0.4 - - - -
43L GLY* 4.0 22.7 - - - +
82L ILE* 4.6 10.1 - - + -
84L LEU* 4.1 7.2 - - + -
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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