Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 4X8G
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 SER 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A CYS* 3.7 3.2 - - - +
38A THR* 1.3 90.1 + - - +
40A PHE* 1.3 66.1 + - - +
67A THR* 4.1 16.1 - - - +
68A TRP 3.3 15.3 + - - -
69A PRO* 4.2 4.3 - - - +
70A LEU* 4.4 4.5 - - - -
96A TYR* 3.8 1.9 - - - +
97A TYR* 2.9 38.4 + - - +
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Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 27.4 - - + -
30A CYS* 5.7 4.0 - - - -
39A SER* 1.3 79.7 - - - +
41A SER* 1.3 61.0 + - - +
42A ILE* 3.5 33.0 - - + -
52A ILE* 4.3 9.0 - - + -
67A THR* 2.9 16.0 + - - -
68A TRP* 3.1 39.7 + + + +
70A LEU* 3.8 25.4 - - + -
74A VAL* 4.3 20.4 - - + -
76A VAL* 4.5 7.0 - - + -
94A ILE* 4.4 6.3 - - + -
95A SER 3.3 15.7 - - - +
96A TYR* 4.2 13.2 - + + -
97A TYR* 3.9 4.5 - - - -
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Residues in contact with SER 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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40A PHE* 1.3 78.0 - - - +
42A ILE* 1.3 71.7 + - - +
43A ASN 4.4 0.2 + - - -
66A SER 5.0 3.1 + - - -
67A THR* 4.1 13.9 - - - -
68A TRP* 5.1 4.7 + - - -
93A GLN 4.1 0.3 - - - +
95A SER* 3.0 36.1 + - - +
97A TYR* 3.8 17.6 - - - -
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Residues in contact with ILE 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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27A LEU* 5.4 5.4 - - + -
40A PHE* 3.5 37.5 - - + -
41A SER* 1.3 88.2 + - - +
43A ASN* 1.3 68.8 + - - +
50A VAL* 5.0 21.9 - - + +
52A ILE* 4.6 13.7 - - + -
68A TRP* 4.7 5.0 - - + +
76A VAL* 4.8 12.1 - - + -
92A VAL* 3.8 23.6 - - + -
93A GLN 3.4 12.6 - - - +
94A ILE* 4.4 14.6 - - + -
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Residues in contact with ASN 43 (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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42A ILE* 1.3 78.3 - - - +
44A ALA* 1.3 82.8 + - - +
50A VAL* 6.2 0.4 - - - -
92A VAL* 3.9 0.2 - - - -
93A GLN* 2.9 42.9 + - - +
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Residues in contact with ALA 44 (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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43A ASN* 1.3 91.2 + - - +
45A SER* 1.3 66.7 + - - +
46A PRO* 4.4 1.4 - - - +
48A VAL* 3.9 19.5 - - + +
50A VAL* 4.6 11.8 - - + +
91A LYS 3.4 15.5 - - - +
92A VAL* 3.7 18.8 - - + -
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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