Contacts of the strand formed by residues 48 - 56 (chain A) in PDB entry 4M7A
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 GLU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.1 4.8 - - - -
43A ASN* 2.8 26.6 + - + +
46A SER* 3.4 28.0 + - - +
47A LYS* 1.3 76.9 - - - +
49A PHE* 1.3 67.3 + - - +
50A ILE* 3.2 10.7 + - + +
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Residues in contact with PHE 49 (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 ASN* 3.4 29.6 - - - -
41A VAL 3.4 10.3 - - - -
42A PHE* 4.3 5.2 - - + +
47A LYS 4.2 1.4 + - - -
48A GLU* 1.3 76.5 - - - +
50A ILE* 1.3 63.1 + - - +
51A SER* 3.2 37.2 - - - -
52A LYS* 3.4 36.8 - - + -
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Residues in contact with ILE 50 (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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21A GLU* 6.1 0.4 - - - +
23A LEU* 3.6 30.7 - - + -
41A VAL* 3.0 10.2 + - + +
42A PHE* 4.3 3.8 - - - +
43A ASN* 4.2 15.5 - - + +
48A GLU* 3.7 15.3 - - + +
49A PHE* 1.3 75.1 - - - +
51A SER* 1.3 64.4 + - - +
54A GLN* 3.9 16.4 - - - +
78G PHE* 5.5 4.0 - - + -
80G LYS* 3.3 42.4 + - - +
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Residues in contact with SER 51 (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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41A VAL* 2.8 29.9 + - - +
49A PHE* 3.2 17.3 - - - -
50A ILE* 1.3 84.2 + - - +
52A LYS* 1.3 65.7 + - - +
53A ALA* 3.4 23.2 + - - -
54A GLN* 4.3 14.4 - - - -
80G LYS* 4.4 12.2 - - - +
81G LEU 3.9 9.9 + - - -
83G ASP* 4.8 2.8 + - - -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A THR* 3.1 12.4 - - - +
40A ASN* 2.8 47.7 + - - +
41A VAL* 5.4 0.2 - - - -
49A PHE* 3.4 32.3 - - + -
51A SER* 1.3 77.0 + - - +
53A ALA* 1.3 59.3 + - - +
83G ASP* 3.9 36.0 + - + +
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Residues in contact with ALA 53 (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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37A PHE* 4.4 5.8 - - + -
38A LEU 3.3 8.3 - - - +
39A THR* 4.5 4.9 - - + -
41A VAL* 5.6 0.2 - - - -
51A SER* 3.4 9.5 + - - -
52A LYS* 1.3 81.4 - - + +
54A GLN* 1.3 64.5 + - - +
81G LEU* 3.1 31.9 + - + +
82G GLN 4.7 2.9 - - - +
83G ASP* 5.1 2.4 + - - -
85G ILE* 3.5 32.8 - - + -
86G ILE* 5.1 1.3 - - + -
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Residues in contact with GLN 54 (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* 4.2 21.0 - - - +
37A PHE* 3.9 1.6 - - - -
38A LEU* 2.8 42.7 + - + +
41A VAL* 4.3 20.0 - - + +
50A ILE* 3.9 25.7 - - - +
51A SER* 4.3 8.1 - - - -
53A ALA* 1.3 76.3 - - - +
55A LEU* 1.3 63.5 + - - +
56A LEU* 4.1 7.3 + - - +
78G PHE* 4.0 31.7 - - - +
79G ILE 3.3 11.2 - - - +
80G LYS* 4.0 11.2 - - - +
81G LEU* 4.4 6.8 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ASN* 4.6 0.2 - - + -
36A LEU 3.8 5.2 - - - +
37A PHE* 4.9 3.1 - - - +
54A GLN* 1.3 73.4 - - - +
56A LEU* 1.3 75.1 + - - +
57A ARG* 4.9 1.8 - - + +
3G PRO* 4.0 29.6 - - + +
6G LEU* 5.2 4.5 - - + -
7G LEU* 3.5 44.4 - - + -
36G MET* 3.7 26.5 - - + -
78G PHE* 3.1 6.5 - - - +
79G ILE* 2.6 56.3 + - + +
81G LEU* 4.5 9.4 - - + +
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Residues in contact with LEU 56 (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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15A ILE* 4.4 6.7 - - + -
17A LEU* 3.8 22.4 - - + -
23A LEU* 4.0 21.8 - - + -
35A ASN* 3.3 5.4 - - - +
36A LEU* 2.9 40.1 + - + +
38A LEU* 4.1 19.7 - - + -
54A GLN* 4.1 4.5 + - - +
55A LEU* 1.3 78.7 - - - +
57A ARG* 1.3 70.9 + - - +
60A GLU* 3.9 18.6 - - + -
61A ILE* 3.5 18.2 - - + -
77G LYS 3.3 14.1 - - - +
78G PHE* 3.7 17.0 - - + -
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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