Contacts of the strand formed by residues 52 - 58 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23Q GLY* 3.9 15.5 - - - -
24Q LEU 3.5 3.1 - - - +
26Q ARG* 3.3 2.3 + - - -
33Q HIS* 2.6 22.9 + - - -
47Q GLN 4.5 1.3 - - - +
48Q PHE* 3.5 6.4 - - + -
49Q THR* 2.9 38.2 + - - +
51Q HIS* 1.3 76.8 - - - +
53Q SER* 1.3 57.2 + - - +
54Q ALA 3.5 21.8 - - - +
55Q ILE* 3.9 17.0 - - + -
101R TRP* 2.9 27.3 + - + +
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Residues in contact with SER 53 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47P GLN* 3.1 35.0 + - - +
49P THR* 3.7 11.9 - - - -
24Q LEU 3.3 4.4 + - - -
25Q THR 3.8 0.2 + - - -
26Q ARG* 3.3 38.5 + - - +
48Q PHE* 3.9 6.2 - - - -
52Q THR* 1.3 74.2 - - - +
54Q ALA* 1.3 61.9 + - - +
101Q TRP* 2.9 33.3 + - - +
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Residues in contact with ALA 54 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P LEU* 4.3 4.5 - - + -
45P ILE 3.1 12.6 - - - +
46P ALA* 4.0 12.3 - - + -
24Q LEU* 2.9 52.7 + - + -
48Q PHE* 3.9 1.5 - - - -
52Q THR* 3.5 7.9 - - - +
53Q SER* 1.3 82.8 + - - +
55Q ILE* 1.3 63.1 + - - +
101Q TRP* 4.1 16.2 - - + -
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Residues in contact with ILE 55 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P VAL 3.9 0.7 - - - +
44P LEU* 3.5 4.6 - - - +
45P ILE* 2.8 46.4 + - + +
10Q VAL* 4.0 22.9 - - + -
12Q ILE* 4.6 3.6 - - + -
21Q VAL* 3.8 28.7 - - + -
22Q ILE 3.3 5.8 - - - +
46Q ALA* 4.4 8.7 - - + +
47Q GLN 4.4 4.0 - - - +
48Q PHE* 3.8 25.8 - - + -
52Q THR* 3.9 10.5 - - + -
54Q ALA* 1.3 81.5 - - - +
56Q LYS* 1.4 62.3 + - - +
57Q VAL* 4.3 10.3 - - + -
101R TRP* 3.9 19.1 - - + -
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Residues in contact with LYS 56 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P GLU* 2.7 31.3 + - + +
37P LYS 3.8 2.8 + - - -
38P LEU* 3.8 16.6 - - + -
42P GLU* 3.8 22.1 + - + +
43P VAL 3.3 9.0 - - - +
44P LEU* 4.1 6.1 - - + -
20Q ASN 3.7 1.0 - - - +
21Q VAL* 3.7 1.7 - - - -
22Q ILE* 2.8 53.6 + - + +
24Q LEU* 4.0 14.4 - - + +
32Q PHE* 4.4 6.1 - - + -
55Q ILE* 1.4 72.9 - - - +
57Q VAL* 1.4 67.7 + - - +
58Q ARG* 3.2 24.0 - - + +
127W A 3.7 8.3 - - - +
128W G 2.9 19.0 + - - -
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Residues in contact with VAL 57 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P GLU* 3.8 9.5 - - - +
43P VAL* 2.9 31.2 + - + +
45P ILE* 4.7 6.7 - - + -
12Q ILE* 4.2 24.9 - - + -
19Q VAL* 4.1 10.1 - - + -
20Q ASN 3.4 8.3 - - - +
21Q VAL* 4.7 3.4 - - + -
55Q ILE* 4.3 10.1 - - + -
56Q LYS* 1.4 77.3 - - - +
58Q ARG* 1.3 63.4 + - - +
61Q ALA* 3.9 16.2 - - + -
63Q ILE* 4.0 22.2 - - + -
72Q SER* 3.5 25.6 - - - +
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Residues in contact with ARG 58 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P GLU* 3.1 32.8 + - - +
18Q GLY 5.4 0.7 - - - -
19Q VAL* 3.4 5.9 - - - +
20Q ASN* 2.9 45.9 + - + +
22Q ILE* 3.8 23.7 - - + +
32Q PHE* 4.1 4.6 - - - -
56Q LYS* 3.2 28.3 - - + +
57Q VAL* 1.3 75.5 - - - +
59Q GLY* 1.3 62.6 + - - +
126W G 6.1 1.2 - - - +
127W A 5.1 1.0 - - - +
128W G 3.3 13.5 + - - -
129W U 2.9 41.5 + - - +
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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