Contacts of the strand formed by residues 52 - 58 (chain V) in PDB entry 5EF3
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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101L TRP* 2.8 31.1 + - + +
23V GLY* 3.9 13.2 - - - -
24V LEU 3.4 5.6 - - - +
26V ARG* 3.4 1.7 + - - -
33V HIS* 2.5 23.8 + - - -
47V GLN 4.7 1.6 - - - +
48V PHE* 3.6 6.0 - - + -
49V THR* 3.0 35.7 + - - +
51V HIS* 1.3 77.4 - - - +
53V SER* 1.3 58.2 + - - +
54V ALA 3.4 22.9 - - - +
55V ILE* 3.9 16.4 - - + -
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Residues in contact with SER 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U GLN* 3.1 35.9 + - - +
49U THR* 3.9 9.0 - - - -
24V LEU 3.2 5.1 + - - -
25V THR 3.8 0.3 + - - -
26V ARG* 3.3 42.5 + - - +
48V PHE* 3.9 5.8 - - - -
52V THR* 1.3 73.1 - - - +
54V ALA* 1.3 59.9 + - - +
101V TRP* 3.1 32.2 + - - +
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Residues in contact with ALA 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U LEU* 4.3 4.5 - - + -
45U ILE 3.1 13.2 - - - +
46U ALA* 4.1 11.2 - - + -
24V LEU* 2.8 55.2 + - + -
48V PHE* 3.9 2.7 - - - -
52V THR* 3.4 8.6 - - - +
53V SER* 1.3 81.1 + - - +
55V ILE* 1.4 60.9 + - - +
101V TRP* 4.2 16.8 - - + -
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Residues in contact with ILE 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L TRP* 4.0 17.5 - - + -
43U VAL 3.8 1.0 - - - +
44U LEU* 3.5 3.7 - - - -
45U ILE* 2.8 50.1 + - + +
10V VAL* 4.0 21.8 - - + -
12V ILE* 4.6 4.9 - - + -
21V VAL* 3.8 28.7 - - + -
22V ILE 3.3 6.7 - - - +
46V ALA* 4.4 9.2 - - + +
47V GLN 4.5 3.4 - - - +
48V PHE* 3.8 27.8 - - + -
52V THR* 3.9 10.1 - - + -
54V ALA* 1.4 81.2 - - - +
56V LYS* 1.3 65.2 + - - +
57V VAL* 4.2 8.9 + - + -
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Residues in contact with LYS 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U GLU* 2.8 30.3 + - - +
37U LYS 4.0 2.2 + - - -
38U LEU* 3.9 16.4 - - + -
42U GLU* 3.8 26.2 + - + -
43U VAL 3.2 9.9 - - - +
44U LEU* 4.1 6.5 - - + -
20V ASN 3.6 2.3 - - - +
21V VAL* 3.7 1.7 - - - -
22V ILE* 2.8 50.1 + - + +
24V LEU* 3.9 14.7 - - + +
32V PHE* 4.8 5.6 - - + -
55V ILE* 1.3 75.1 - - - +
57V VAL* 1.3 68.1 + - - +
58V ARG* 3.3 21.4 - - + +
152W A 3.7 7.3 - - - +
153W G 2.9 19.4 + - - -
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Residues in contact with VAL 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42U GLU* 3.8 9.5 - - - +
43U VAL* 2.8 33.9 + - + +
45U ILE* 4.8 6.5 - - + -
12V ILE* 4.2 25.8 - - + -
19V VAL* 4.2 10.1 - - + -
20V ASN 3.4 7.6 - - - +
21V VAL* 4.7 4.0 - - + -
55V ILE* 4.4 8.5 - - + -
56V LYS* 1.3 78.2 - - - +
58V ARG* 1.3 64.3 + - - +
61V ALA* 4.1 15.5 - - + -
63V ILE* 3.9 23.6 - - + -
72V SER* 3.6 24.5 - - - +
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Residues in contact with ARG 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U ASP* 6.0 0.4 + - - -
42U GLU* 3.3 29.4 + - - +
18V GLY 4.5 0.6 - - - +
19V VAL* 3.3 7.8 - - - +
20V ASN* 2.9 57.0 + - + +
22V ILE* 3.5 28.8 - - + +
32V PHE* 3.9 13.3 - - - -
56V LYS* 3.3 29.0 + - - +
57V VAL* 1.3 73.9 - - - +
59V GLY* 1.3 62.9 + - - +
151W G 5.4 5.9 - - - +
152W A 4.9 3.4 + - - +
153W G 3.6 11.1 + - - -
154W U 4.5 12.9 + - - +
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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