Contacts of the strand formed by residues 30 - 36 (chain A) in PDB entry 1O5L
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 ASP 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.5 10.0 - - - +
28A ILE* 3.8 16.5 - - - +
29A GLU* 1.3 87.6 + - - +
31A VAL* 1.3 64.1 + - - +
32A LEU* 3.6 16.5 + - + +
74A PHE* 4.8 2.4 - - - -
88A SER* 2.7 33.4 + - - +
89A ILE 3.4 15.0 - - - +
90A PRO* 3.4 20.8 - - - +
91A LYS* 5.1 0.7 - - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 1.3 70.8 - - - +
32A LEU* 1.3 62.4 + - - +
33A ILE* 4.6 9.3 - - + +
61A ILE* 3.8 24.9 - - + -
67A ILE* 4.0 32.5 - - + -
68A PHE* 4.9 0.4 - - + -
87A LEU 3.4 4.3 - - - +
88A SER* 3.4 1.4 - - - -
89A ILE* 2.9 41.0 + - + +
91A LYS* 4.3 8.3 - - + -
94A PHE* 3.8 52.9 - - + -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 5.4 3.8 - - + -
21A VAL* 4.4 14.8 - - + -
22A LYS* 4.1 22.2 - - + -
30A ASP* 3.6 16.5 + - + +
31A VAL* 1.3 78.4 - - - +
33A ILE* 1.3 61.0 + - - +
34A LEU 4.3 0.2 - - - -
61A ILE* 3.4 6.9 - - - +
62A ILE* 2.9 52.3 + - + +
74A PHE* 3.8 28.7 - - + -
86A ILE* 4.1 11.7 - - + -
87A LEU 3.3 2.0 - - - -
88A SER* 3.6 28.9 - - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.2 15.0 - - + +
6A LEU* 4.3 15.5 - - + -
31A VAL* 4.6 9.0 - - + +
32A LEU* 1.3 78.8 - - - +
34A LEU* 1.3 64.2 + - - +
35A LEU* 3.4 7.2 + - + +
59A VAL* 3.7 27.1 - - + -
60A GLN 3.4 13.5 - - - +
61A ILE* 4.0 20.2 - - + -
62A ILE* 4.9 0.2 - - - -
86A ILE* 3.3 5.4 - - - +
87A LEU* 2.8 57.6 + - + +
89A ILE* 4.2 24.7 - - + -
94A PHE* 5.0 2.2 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 4.3 0.2 - - - -
33A ILE* 1.3 70.7 - - - +
35A LEU* 1.3 59.2 + - - +
36A GLU 3.4 23.1 - - - +
37A GLY 4.2 4.5 - - - +
39A LEU* 3.8 36.1 - - + +
56A ILE* 3.2 37.5 - - + +
57A LYS* 3.5 20.2 - - - +
58A PRO* 3.5 11.4 - - + +
59A VAL* 3.2 30.5 - - - +
60A GLN 2.9 16.5 + - - +
62A ILE* 4.5 3.7 - - + +
84A SER* 4.3 4.0 - - - +
85A LYS 3.6 9.0 - - - +
86A ILE* 4.1 8.1 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU 5.6 0.2 - - - +
4A LYS* 3.7 45.6 + - + -
7A LEU* 3.9 30.5 - - + -
12A VAL* 4.3 9.0 - - + -
33A ILE* 3.9 9.0 - - + +
34A LEU* 1.3 73.7 - - - +
36A GLU* 1.3 71.2 + - + +
58A PRO* 3.4 12.1 - - - +
59A VAL* 4.1 4.2 - - + +
85A LYS* 2.9 17.1 + - + +
86A ILE 3.9 10.5 - - - +
87A LEU* 3.9 40.6 - - + +
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 4.7 10.4 + - - +
34A LEU* 3.4 6.3 - - - +
35A LEU* 1.3 86.0 - - + +
37A GLY* 1.3 58.9 + - - +
58A PRO* 3.7 9.6 - - - -
83A ASN 4.7 0.4 - - - -
84A SER* 3.3 6.3 - - - -
85A LYS* 3.0 70.2 + - + +
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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