Contacts of the strand formed by residues 19 - 23 (chain K) in PDB entry 4ZZ7
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 SER 19 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H ARG* 3.5 4.1 - - - +
19H SER* 2.7 49.6 + - - +
33H GLN* 5.3 1.6 + - - -
3K THR* 5.5 3.8 - - - -
18K ARG* 1.3 77.9 - - - +
20K GLN* 1.3 60.4 + - - +
33K GLN* 2.7 32.5 + - - +
34K LEU 3.2 16.6 - - - -
35K ASP* 4.3 2.7 - - - -
36K LEU* 4.2 2.9 - - - -
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Residues in contact with GLN 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H THR* 3.2 18.1 + - - +
18H ARG* 3.0 32.4 + - - +
19K SER* 1.3 75.4 - - - +
21K ASN* 1.3 75.1 + - - +
22K VAL 3.5 0.2 + - - -
33K GLN* 3.4 6.5 - - - -
34K LEU* 2.7 48.5 + - + +
36K LEU* 4.0 13.5 - - + +
175K GLU* 3.8 34.2 + - - +
176K ARG* 5.3 6.1 - - - +
204K ASP* 5.0 3.5 - - - +
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Residues in contact with ASN 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ASN* 2.7 34.8 + - - +
17H THR* 2.8 19.6 + - - +
18H ARG* 5.4 0.7 - - - -
19H SER* 5.7 0.3 + - - -
20K GLN* 1.3 85.2 + - - +
22K VAL* 1.3 61.9 + - - +
23K PHE* 3.5 25.9 - - + -
30K ILE* 3.1 31.5 - - + +
32K LYS 3.8 4.3 - - - -
33K GLN* 2.5 32.1 + - - +
175K GLU 4.8 2.4 - - - +
176K ARG* 5.8 0.9 - - - -
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Residues in contact with VAL 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K ILE* 4.8 1.8 - - + -
20K GLN* 4.1 0.4 - - + +
21K ASN* 1.3 76.7 - - - +
23K PHE* 1.3 61.6 + - - +
30K ILE* 3.7 3.5 - - - +
31K GLY* 2.9 22.7 + - - -
32K LYS* 3.0 43.8 + - + +
33K GLN 4.6 0.9 - - - -
34K LEU* 3.7 29.2 - - + +
89K GLU* 3.9 20.0 - - + +
175K GLU 3.9 13.2 - - - +
176K ARG* 4.4 13.9 - - - +
178K PRO* 4.3 10.8 - - + -
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Residues in contact with PHE 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ASN 4.6 6.1 - - - -
17H THR* 4.8 15.5 - - + -
21K ASN* 3.5 36.8 - - + -
22K VAL* 1.3 81.0 - - - +
24K ASN* 1.3 60.2 + - - +
25K PRO* 3.4 10.9 - - + +
28K GLY 3.4 27.8 - - - -
29K GLU 3.4 8.7 - - - -
30K ILE* 4.0 14.1 - - + -
31K GLY* 4.5 2.7 - - - -
88K GLU 3.7 5.9 - - - +
89K GLU* 3.8 14.2 - - - +
176K ARG 4.9 3.9 + - - +
324K ILE 5.4 3.1 - - - +
325K THR* 5.9 7.2 - - + -
362K PHE* 4.0 28.0 - + + -
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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
------------------------------------------------------------
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