Contacts of the strand formed by residues 35 - 42 (chain A) in PDB entry 3O71
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU* 3.3 6.1 - - - +
32A GLY* 2.8 33.5 + - - +
33A ALA 3.8 0.6 - - - -
34A TYR* 1.3 80.3 - - - +
36A MET* 1.3 58.9 + - - -
52A LYS* 5.6 4.0 - - - -
53A LYS 3.1 13.0 - - - -
54A ILE* 4.6 9.0 - - - -
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Residues in contact with MET 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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12A VAL* 3.3 36.6 - - + +
13A ARG* 4.7 6.3 - - - +
15A GLN* 3.7 15.7 - - + -
17A PHE* 3.2 36.7 - - + -
28A TYR* 3.6 28.3 - - + -
30A GLY 3.5 12.8 - - - +
31A GLU* 4.1 10.8 - - + +
35A GLY* 1.3 73.5 - - - +
37A VAL* 1.3 65.4 + - - +
38A CYS* 4.3 2.2 - - - -
52A LYS* 3.5 3.8 - - - +
53A LYS* 3.0 33.3 + - + -
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Residues in contact with VAL 37 (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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28A TYR* 4.0 0.7 - - - -
29A ILE* 2.9 37.2 + - + -
30A GLY* 2.8 36.4 + - - +
31A GLU* 4.6 0.8 - - - +
36A MET* 1.3 73.3 - - - +
38A CYS* 1.3 73.3 + - - +
50A ALA* 4.5 13.5 - - + -
51A ILE 3.5 15.3 - - - +
52A LYS* 4.3 19.1 - - + -
103A GLN* 5.7 2.7 - - - +
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Residues in contact with CYS 38 (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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12A VAL* 3.8 33.0 - - - -
17A PHE* 3.8 28.5 - - + -
26A LEU* 4.7 7.2 - - + -
27A SER 3.3 16.4 - - - +
28A TYR* 3.9 3.6 - - - -
29A ILE* 3.8 7.2 - - - +
36A MET* 4.3 4.9 - - - -
37A VAL* 1.3 79.9 - - - +
39A SER* 1.3 66.8 + - - +
50A ALA* 3.3 5.4 - - - +
51A ILE* 2.9 36.2 + - + +
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Residues in contact with SER 39 (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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25A ASN 3.5 2.5 + - - +
26A LEU* 3.4 4.9 - - - -
27A SER* 2.8 51.0 + - - -
29A ILE* 3.5 14.2 - - - +
38A CYS* 1.3 75.0 - - - +
40A ALA* 1.3 62.3 + - - +
48A ARG* 3.9 22.9 + - - -
49A VAL 3.5 5.2 - - - -
105A LEU* 3.8 20.9 - - - -
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Residues in contact with ALA 40 (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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23A TYR* 4.7 1.1 - - + -
24A THR 3.5 2.2 - - - +
25A ASN 3.5 9.6 - - - -
26A LEU* 3.3 25.6 - - + -
38A CYS 4.8 0.4 - - - +
39A SER* 1.3 75.9 - - - +
41A TYR* 1.3 60.7 + - - +
48A ARG* 3.3 11.0 + - - +
49A VAL* 2.7 43.4 + - + +
51A ILE* 4.0 22.0 - - + -
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Residues in contact with TYR 41 (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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22A ARG 3.5 2.3 - - - +
23A TYR* 3.4 6.3 - - - -
24A THR* 2.9 34.7 + - - +
25A ASN* 4.1 20.8 + - + +
40A ALA* 1.3 73.3 - - - +
42A ASP* 1.3 63.6 + - - +
43A ASN* 3.3 31.4 + - - -
46A LYS* 3.3 31.0 + - - +
47A VAL* 3.7 25.8 - - - -
48A ARG* 4.3 14.1 - - + +
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Residues in contact with ASP 42 (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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22A ARG* 2.9 47.0 + - - +
23A TYR* 3.8 18.4 - - + -
40A ALA 4.1 0.6 + - - -
41A TYR* 1.3 71.7 - - - +
43A ASN* 1.3 59.2 + - - +
44A LEU 3.1 8.0 + - - -
45A ASN* 3.4 24.9 + - - +
46A LYS* 3.0 29.6 + - - -
47A VAL* 2.7 23.6 + - + +
49A VAL* 4.0 13.6 - - + +
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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