Contacts of the strand formed by residues 19 - 25 (chain C) 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 VAL 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ALA* 3.9 8.1 - - + -
16C GLU* 3.6 20.2 - - + +
18C GLY* 1.3 78.0 - - - +
20C ASN* 1.3 63.8 + - - +
21C VAL* 4.4 0.7 - - + -
36C GLU 3.6 0.7 - - - +
37C LYS* 3.3 4.7 - - - -
38C LEU* 2.8 52.2 + - + +
57C VAL* 4.0 20.9 - - + -
58C ARG 3.4 10.3 - - - +
59C GLY* 4.0 2.2 - - - -
60C LYS 3.3 38.4 - - - +
61C ALA* 4.4 7.4 - - + -
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Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLY 3.8 11.3 + - - +
19C VAL* 1.3 79.9 - - - +
21C VAL* 1.3 61.6 + - - +
22C ILE* 3.9 14.9 + - + +
35C SER* 3.4 21.4 + - - +
36C GLU 3.6 2.7 - - - -
37C LYS* 4.2 12.8 - - - +
56C LYS 3.6 1.4 - - - +
57C VAL* 3.4 5.9 - - - +
58C ARG* 2.9 49.5 + - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 4.2 13.4 - - + -
12C ILE* 3.5 39.3 - - + -
19C VAL* 4.4 2.5 - - + -
20C ASN* 1.3 74.3 - - - +
22C ILE* 1.3 60.8 + - - +
23C GLY 3.9 1.4 + - - -
34C HIS 3.9 0.3 - - - +
35C SER* 3.5 0.7 - - - -
36C GLU* 2.9 40.8 + - + +
38C LEU* 3.6 31.0 - - + -
44C LEU* 3.7 20.2 - - + -
46C ALA* 5.1 0.7 - - + -
55C ILE* 3.9 16.4 - - + -
56C LYS 3.6 2.9 - - - +
57C VAL* 4.7 2.9 - - + +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 4.0 2.2 - - - -
20C ASN* 4.1 17.3 - - + -
21C VAL* 1.3 75.2 - - - +
23C GLY* 1.3 61.0 + - - +
24C LEU* 3.6 2.2 - - + +
32C PHE* 3.3 50.7 - - + -
34C HIS 3.4 7.2 - - - +
35C SER* 3.9 18.8 - - - +
55C ILE* 3.4 5.5 - - - -
56C LYS* 2.8 50.3 + - + +
58C ARG* 3.7 41.3 - - + +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B TRP* 3.4 28.5 - - - -
22C ILE* 1.3 72.4 - - - +
24C LEU* 1.3 60.0 + - - -
32C PHE* 3.5 4.9 - - - -
33C HIS* 3.0 37.7 + - - -
34C HIS 2.9 11.5 + - - +
52C THR* 4.0 3.1 - - - -
54C ALA 3.8 4.0 - - - -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE 3.6 16.4 - - - +
23C GLY* 1.3 75.6 - - - -
25C THR* 1.4 66.2 + - - +
30C THR* 3.7 21.3 - - + -
31C ARG 3.4 5.8 - - - +
32C PHE* 3.8 25.8 - - + -
33C HIS* 3.7 2.7 - - - -
52C THR* 3.4 5.5 - - - -
53C SER 3.2 19.8 + - - -
54C ALA* 2.8 40.0 + - + +
55C ILE 4.5 0.2 - - - +
56C LYS* 4.1 13.2 - - + +
101C TRP* 5.2 2.9 - - + -
34D HIS* 5.0 0.4 - - + +
36D GLU* 3.7 31.0 - - + +
44D LEU* 4.3 7.4 - - + -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 1.4 71.5 - - - +
26C ARG* 1.3 63.6 + - - +
29C ASP 2.9 24.5 + - - -
30C THR* 4.3 0.9 - - - -
31C ARG* 2.9 55.0 + - + +
33C HIS* 3.8 25.4 - - + -
51C HIS 3.4 7.2 - - - +
53C SER* 3.7 2.5 + - - -
101C TRP* 2.8 25.6 + - - +
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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