Contacts of the strand formed by residues 19 - 25 (chain B) in PDB entry 4ZDH
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 4.5 5.6 - - + -
13B LYS* 3.6 42.8 - - + +
17B GLU* 3.7 13.2 - - + +
18B LYS* 1.3 78.8 - - - +
20B PHE* 1.3 66.1 + - - +
21B LEU* 3.9 23.6 - - + -
76B LEU 3.6 1.4 - - - +
77B ILE* 3.3 5.1 - - - +
78B LEU* 2.8 51.5 + - + +
81B ALA* 4.2 9.9 - - + -
110B LEU* 4.4 15.0 - - + -
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Residues in contact with PHE 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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7B SER* 4.5 3.6 + - - -
8B SER* 5.6 0.9 + - - -
11B LEU* 4.7 3.6 - - - +
13B LYS* 5.7 0.8 - - - +
18B LYS* 3.5 46.2 - - + -
19B VAL* 1.3 79.4 - - - +
21B LEU* 1.3 70.2 + - - +
22B GLU* 3.8 21.3 + - + +
75B SER* 5.3 3.6 - - - -
76B LEU 3.4 2.0 - - - -
77B ILE* 3.9 33.7 - - + -
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Residues in contact with LEU 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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7B SER* 4.1 3.1 - - - +
8B SER* 5.7 0.4 - - - -
11B LEU* 3.4 29.6 - - + -
19B VAL* 3.9 12.3 - - + -
20B PHE* 1.3 86.2 - - - +
22B GLU* 1.3 62.8 + - - +
34B TRP* 3.7 17.9 - - + -
75B SER* 3.5 3.1 - - - -
76B LEU* 2.7 57.3 + - + +
78B LEU* 4.7 5.8 - - + -
89B TYR* 3.7 43.1 - - + -
108B THR* 4.4 16.2 - - + +
110B LEU* 5.1 3.8 - - + -
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Residues in contact with GLU 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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6B GLN* 3.1 9.9 - - - +
7B SER* 2.8 53.3 + - - +
20B PHE* 3.8 26.6 - - + +
21B LEU* 1.3 76.5 - - - +
23B CYS* 1.3 60.2 + - - +
24B VAL* 4.7 4.7 - - + -
34B TRP* 4.0 3.3 - - - -
73B ARG* 3.2 39.1 - - - +
74B PHE 4.3 0.2 - - - -
75B SER* 2.7 30.9 + - - -
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Residues in contact with CYS 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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4B VAL* 3.8 11.4 - - - -
5B THR 3.4 3.8 - - - -
22B GLU* 1.3 73.4 - - - +
24B VAL* 1.3 62.9 + - - +
32B MET* 3.5 23.3 - - + +
33B PHE 5.2 0.4 - - - -
34B TRP* 3.6 4.5 - - + +
72B GLU 3.6 0.5 - - - +
73B ARG* 3.2 5.0 - - - +
74B PHE* 2.9 44.2 + - + +
91B CYS* 2.1 55.2 - - + -
92B ALA 4.4 2.9 - - - -
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Residues in contact with VAL 24 (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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3B LYS 4.3 0.3 - - - +
4B VAL* 3.7 0.9 - - - -
5B THR* 2.9 46.5 + - - +
22B GLU* 4.7 2.7 - - + -
23B CYS* 1.3 82.0 - - - +
25B GLN* 1.3 65.1 + - - +
26B ASP* 4.4 11.0 - - - +
32B MET* 4.8 0.7 - - - -
72B GLU* 3.1 24.5 - - + +
73B ARG* 3.6 42.8 - - + +
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Residues in contact with GLN 25 (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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3B LYS 3.7 14.1 - - - +
4B VAL* 4.3 6.7 - - + -
24B VAL* 1.3 74.1 - - - +
26B ASP* 1.3 61.7 + - - +
27B MET* 3.1 29.8 + - + +
28B ASP* 3.1 3.7 + - - +
29B HIS* 3.0 54.8 + - - +
32B MET* 3.7 25.1 - - + -
71B LYS* 3.3 20.8 + - - +
72B GLU* 2.9 27.0 + - - +
93B SER* 4.0 10.3 - - - +
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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