Contacts of the strand formed by residues 17 - 23 (chain B) in PDB entry 2Z21
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ALA 3.6 1.6 - - - +
13B ILE* 3.3 7.6 - - - -
14B GLN* 2.9 39.4 + - + +
15B GLY 3.4 1.0 + - - -
16B SER* 1.3 87.3 - - - +
18B LEU* 1.3 62.4 + - - +
19B THR* 3.9 8.3 + - - +
33B SER* 3.7 29.4 - - - +
34B ILE 3.5 8.7 - - - +
35B ASP* 4.5 12.6 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.9 26.9 - - + -
11B SER* 4.2 16.6 - - - -
12B ALA 3.4 15.0 - - - +
13B ILE* 4.0 12.8 - - + -
16B SER 3.9 1.2 + - - -
17B VAL* 1.3 71.9 - - - +
19B THR* 1.3 68.3 + - - +
20B SER* 5.1 0.2 - - - -
33B SER* 3.2 3.1 - - - -
34B ILE* 2.8 56.9 + - + +
36B LEU* 4.0 15.7 - - + +
63B LEU* 4.7 3.1 - - + -
87B LEU* 4.1 16.6 - - + -
91B ILE* 4.1 11.2 - - + -
98B LEU* 3.9 15.1 - - + +
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN 4.0 2.4 - - - +
11B SER* 3.2 3.6 - - - -
12B ALA* 3.0 39.1 + - - +
17B VAL* 3.9 8.5 + - - +
18B LEU* 1.3 74.2 - - - +
20B SER* 1.3 65.9 + - - +
31B THR* 3.8 21.5 - - + -
32B SER 3.4 12.3 - - - +
33B SER* 2.6 21.8 + - - +
98B LEU* 4.3 0.2 - - - -
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 4.5 3.1 - - - -
8B CYS* 3.2 17.5 - - - +
9B TYR 3.3 5.8 + - - -
10B ASN 4.5 1.6 - - - -
11B SER* 2.7 25.5 + - - +
18B LEU* 5.1 0.2 - - - -
19B THR* 1.3 77.9 - - - +
21B THR* 1.3 68.1 + - - +
22B CYS* 4.0 11.3 + - - -
30B ASN 3.9 1.0 - - - +
31B THR* 3.4 5.0 - - - +
32B SER* 3.0 33.6 + - - +
98B LEU* 3.7 19.1 - - - +
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Residues in contact with THR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B CYS* 3.2 0.5 - - - -
9B TYR* 2.6 50.2 + - + +
10B ASN* 4.7 14.7 + - - +
20B SER* 1.3 76.4 + - - +
22B CYS* 1.3 61.1 + - - +
29B TYR* 3.9 26.2 - - + -
30B ASN 3.4 6.5 - - - +
31B THR* 2.7 28.1 + - - +
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Residues in contact with CYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA 3.4 4.7 - - - +
8B CYS* 2.0 47.1 - - - -
20B SER* 3.9 10.5 - - - -
21B THR* 1.3 75.4 - - - +
23B ILE* 1.3 63.9 + - - +
24B ARG 3.4 0.2 + - - -
29B TYR* 3.3 7.4 - - - -
30B ASN 2.9 30.9 + - - +
93B ALA* 4.1 7.2 - - + -
96B GLY* 3.8 26.8 - - - +
98B LEU* 4.0 18.4 - - - -
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ALA* 2.8 30.7 + - + +
9B TYR* 3.6 28.5 - - + +
22B CYS* 1.3 72.4 - - - +
24B ARG* 1.3 74.0 + - - +
25B THR* 3.9 0.9 + - - +
27B GLY* 5.0 6.5 - - - -
28B GLY 3.4 10.3 - - - +
29B TYR* 3.4 29.6 - - + +
93B ALA* 5.6 1.0 - - - +
95B ASP* 5.0 0.2 - - - -
96B GLY* 3.8 9.3 + - - -
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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