Contacts of the strand formed by residues 52 - 58 (chain P) in PDB entry 5EEZ
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 THR 52 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23P GLY* 3.8 9.0 - - - -
24P LEU 3.5 2.9 - - - -
26P ARG* 3.5 1.3 + - - -
33P HIS* 2.5 24.8 + - - -
47P GLN 4.5 1.6 - - - +
48P PHE* 3.5 6.5 - - + -
49P THR* 2.9 39.6 + - - +
51P HIS* 1.3 74.6 - - - +
53P SER* 1.3 58.8 + - - +
54P ALA 3.5 21.1 - - - +
55P ILE* 3.9 9.2 - - + -
101Q TRP* 2.9 41.4 + - + +
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Residues in contact with SER 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O GLN* 3.1 36.2 + - - +
49O THR* 3.8 6.5 - - - -
24P LEU 3.2 4.9 + - - -
25P THR 3.8 0.3 + - - -
26P ARG* 3.4 36.6 + - - +
48P PHE* 3.8 6.7 - - - -
52P THR* 1.3 72.9 - - - +
54P ALA* 1.3 60.4 + - - +
101P TRP* 2.8 42.0 + - - +
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Residues in contact with ALA 54 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O LEU* 4.4 4.9 - - + -
45O ILE 3.1 12.3 - - - +
46O ALA* 4.1 8.7 - - + -
24P LEU* 2.7 54.0 + - + -
48P PHE* 3.9 1.3 - - - -
52P THR* 3.5 3.4 - - - +
53P SER* 1.3 83.1 + - - +
55P ILE* 1.3 64.4 + - - +
101P TRP* 4.0 20.9 - - + -
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Residues in contact with ILE 55 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O VAL 3.8 1.0 - - - +
44O LEU* 3.5 5.2 - - - +
45O ILE* 2.8 44.1 + - + +
10P VAL* 4.0 22.7 - - + -
12P ILE* 4.5 4.5 - - + -
21P VAL* 3.7 29.4 - - + -
22P ILE 3.3 5.8 - - - +
46P ALA* 4.4 9.2 - - + +
47P GLN 4.4 3.8 - - - +
48P PHE* 3.8 24.2 - - + -
52P THR* 3.9 11.2 - - + -
54P ALA* 1.3 81.0 - - - +
56P LYS* 1.3 65.4 + - - +
57P VAL* 4.4 7.6 - - + -
101Q TRP* 3.9 18.6 - - + -
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Residues in contact with LYS 56 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O GLU* 2.7 30.8 + - - +
37O LYS 4.0 1.4 + - - -
38O LEU* 4.0 13.9 - - + -
42O GLU* 3.7 24.4 + - + -
43O VAL 3.4 8.1 - - - +
44O LEU* 4.1 9.4 - - + -
20P ASN 3.6 1.2 - - - +
21P VAL* 3.7 0.5 - - - -
22P ILE* 2.8 49.6 + - + +
24P LEU* 3.9 15.2 - - + +
32P PHE* 4.5 12.8 - - + -
55P ILE* 1.3 75.1 - - - +
57P VAL* 1.4 69.7 + - - +
58P ARG* 3.2 20.5 - - + +
122W A 3.9 7.1 - - - +
123W G 2.8 21.8 + - - -
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Residues in contact with VAL 57 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O GLU* 3.8 9.0 - - - +
43O VAL* 2.8 32.6 + - + +
45O ILE* 4.9 5.6 - - + -
12P ILE* 4.2 26.5 - - + -
19P VAL* 4.1 9.2 - - + -
20P ASN 3.3 8.7 - - - +
21P VAL* 4.5 4.0 - - + -
55P ILE* 4.4 8.7 - - + -
56P LYS* 1.4 79.0 - - - +
58P ARG* 1.3 63.4 + - - +
59P GLY 4.3 0.2 + - - -
61P ALA* 4.0 17.7 - - + -
63P ILE* 4.1 20.9 - - + -
72P SER* 3.8 21.2 - - - +
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Residues in contact with ARG 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O GLU* 3.0 34.4 + - - +
18P GLY 4.6 0.7 - - - +
19P VAL* 3.4 6.6 - - - +
20P ASN* 2.9 47.3 + - + +
22P ILE* 3.9 20.8 - - + +
32P PHE* 4.2 1.2 - - - -
56P LYS* 3.2 16.8 + - - +
57P VAL* 1.3 73.5 - - - +
59P GLY* 1.3 62.3 + - - +
121W G 5.6 4.0 - - - +
122W A 4.9 2.8 + - - +
123W G 3.2 27.7 + - - -
124W U 2.7 38.8 + - - +
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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