Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 3O5Z
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 TRP 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.5 33.0 - + - -
18A GLU* 4.2 5.4 - - - -
22A ASP* 4.1 1.3 - - - -
41A LEU* 3.6 19.6 - - - +
54A VAL 3.6 5.7 + - - +
55A GLY* 1.3 79.6 - - - -
57A MET* 1.3 60.1 + - - +
69A ASP* 4.4 9.0 - - + -
70A PHE* 3.4 26.0 - - - -
71A PRO* 3.7 28.8 - - + +
18B GLU 5.0 1.8 + - - -
19B ARG* 3.3 75.0 - - + +
20B PRO* 4.4 15.3 - - + +
21B GLU* 6.4 1.3 - - + -
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Residues in contact with MET 57 (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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9A TYR* 4.1 18.8 - - + -
33A VAL* 4.1 15.5 - - + -
38A LEU* 4.0 19.7 - - + -
41A LEU* 4.5 0.7 - - + -
51A PRO* 3.5 34.3 - - + +
54A VAL* 3.3 30.3 - - + -
55A GLY 4.1 0.2 - - - +
56A TRP* 1.3 73.2 - - - +
58A PRO* 1.4 68.5 - - + +
69A ASP* 3.3 5.4 - - - -
70A PHE* 2.9 60.9 + - + +
72A GLY* 3.8 17.5 - - - -
75A VAL* 4.4 0.2 - - + -
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Residues in contact with PRO 58 (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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33A VAL* 3.5 24.4 - - + +
34A SER 4.9 0.3 + - - -
37A ALA* 3.8 26.6 - - + +
38A LEU* 6.1 0.2 - - + -
41A LEU* 4.1 21.1 - - + -
57A MET* 1.4 86.7 - - + +
59A GLY* 1.3 60.9 + - - +
68A GLY* 3.4 8.7 - - - +
69A ASP* 3.5 16.8 - - - +
70A PHE* 4.2 0.9 - - - -
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Residues in contact with GLY 59 (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 LEU* 3.8 6.8 - - - +
32A VAL 3.4 11.0 - - - -
33A VAL* 4.3 0.4 - - - -
57A MET 4.0 0.2 + - - -
58A PRO* 1.3 77.4 - - - +
60A LEU* 1.3 62.3 + - - -
61A ASN 4.0 0.2 - - - -
67A ARG* 3.1 15.8 - - - +
68A GLY 3.1 31.2 + - - +
70A PHE* 4.0 13.9 - - - -
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Residues in contact with LEU 60 (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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31A LEU* 3.1 7.2 - - - -
32A VAL* 2.8 47.4 + - + +
59A GLY* 1.3 73.3 - - - -
61A ASN* 1.3 69.4 + - - +
62A GLU* 3.7 21.9 + - - +
65A ARG* 3.8 33.7 - - + +
66A GLN 3.5 16.6 - - - +
67A ARG* 3.5 38.3 - - + +
84A ALA* 6.4 2.7 - - + -
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Residues in contact with ASN 61 (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 LEU* 3.8 13.4 - - + +
24A GLU 3.2 20.6 + - - -
25A LEU* 4.1 1.0 - - - +
29A ASP* 3.0 30.0 + - - +
30A VAL 4.3 0.2 - - - +
31A LEU* 3.6 24.0 - - + +
59A GLY 3.9 1.4 + - - -
60A LEU* 1.3 72.5 - - - +
62A GLU* 1.3 54.9 + - - +
63A ARG* 2.9 22.5 + - - +
64A THR* 3.2 25.2 + - - +
65A ARG* 2.7 36.2 + - - -
66A GLN 3.0 8.5 + - - +
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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