Contacts of the strand formed by residues 19 - 25 (chain V) in PDB entry 5EEY
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 VAL 19 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12V ILE* 4.6 0.2 - - + -
14V ALA* 3.6 22.9 - - + -
16V GLU* 3.7 11.4 - - + +
17V ASP 3.5 0.2 - - - -
18V GLY* 1.3 76.9 - - - +
20V ASN* 1.3 72.4 - - - +
21V VAL* 4.4 8.7 - - + -
36V GLU 3.6 0.3 - - - +
37V LYS* 3.3 4.3 - - - -
38V LEU* 2.7 40.1 + - + +
57V VAL* 4.2 14.6 - - + -
58V ARG 3.3 12.1 - - - +
59V GLY* 4.1 1.1 - - - -
60V LYS 3.2 39.5 - - - +
61V ALA* 4.3 7.4 - - + -
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Residues in contact with ASN 20 (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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18V GLY 3.5 7.7 + - - -
19V VAL* 1.3 74.2 - - - +
21V VAL* 1.3 61.9 + - - +
22V ILE* 3.9 17.1 - - + +
35V SER* 3.2 11.8 + - - +
36V GLU 3.4 2.2 - - - -
37V LYS* 3.2 37.9 + - - +
56V LYS 3.6 1.0 - - - +
57V VAL* 3.4 6.9 - - - +
58V ARG* 2.9 58.1 + - + +
154W U 4.9 6.4 + - - +
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Residues in contact with VAL 21 (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* 4.3 12.4 - - + -
12V ILE* 3.6 50.3 - - + -
19V VAL* 4.4 2.5 - - + -
20V ASN* 1.3 76.1 - - - +
22V ILE* 1.3 62.1 + - - +
23V GLY 3.9 0.3 + - - -
34V HIS 3.8 1.0 - - - +
35V SER* 3.7 0.5 - - - -
36V GLU* 2.8 37.7 + - - +
38V LEU* 3.9 19.3 - - + -
44V LEU* 3.7 22.9 - - + -
46V ALA* 5.3 0.9 - - + -
55V ILE* 3.8 17.0 - - + -
56V LYS 3.7 2.7 - - - +
57V VAL* 4.7 3.1 - - + +
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Residues in contact with ILE 22 (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* 4.2 1.6 - - - -
20V ASN* 3.9 16.4 - - + -
21V VAL* 1.3 77.5 - - - +
23V GLY* 1.3 60.6 + - - +
24V LEU* 3.5 7.2 - - + +
32V PHE* 3.4 52.7 - - + -
34V HIS 3.5 10.1 - - - +
35V SER* 3.7 15.0 - - - +
55V ILE* 3.3 6.6 - - - +
56V LYS* 2.8 48.6 + - + +
58V ARG* 3.5 33.4 - - + +
154W U 4.7 2.7 - - - +
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Residues in contact with GLY 23 (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* 3.5 27.5 - - - -
22V ILE* 1.3 70.1 - - - +
24V LEU* 1.3 63.8 + - - -
32V PHE* 3.5 4.5 - - - -
33V HIS* 2.9 35.2 + - - -
34V HIS 2.8 15.0 + - - -
52V THR* 3.9 6.5 - - - -
54V ALA 3.9 4.5 - - - -
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Residues in contact with LEU 24 (chain V).
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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34U HIS* 5.8 0.2 - - + -
36U GLU* 4.0 17.9 - - + +
44U LEU* 3.9 24.2 - - + -
22V ILE* 3.5 28.0 - - + +
23V GLY* 1.3 73.4 - - - -
25V THR* 1.3 66.7 + - - +
30V THR* 4.0 26.0 - - + -
31V ARG 3.4 5.6 - - - +
32V PHE* 4.2 14.1 - - + -
33V HIS* 3.9 1.3 - - - -
52V THR* 3.4 6.8 - - - -
53V SER 3.2 19.9 + - - -
54V ALA* 2.8 30.7 + - + +
56V LYS* 3.9 17.5 - - + +
101V TRP* 6.1 1.1 - - + -
153W G 4.4 2.2 - - - +
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Residues in contact with THR 25 (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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24V LEU* 1.3 74.2 - - - +
26V ARG* 1.4 65.3 + - - +
29V ASP* 2.6 27.4 + - - +
30V THR* 4.2 1.0 - - - -
31V ARG* 2.9 62.5 + - + +
33V HIS* 3.8 27.1 - - + -
51V HIS 3.3 7.0 - - - +
53V SER* 3.8 2.8 + - - -
101V TRP* 2.9 23.7 + - - +
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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