Contacts of the strand formed by residues 38 - 45 (chain H) in PDB entry 1ZWS
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 GLU 38 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H LYS* 2.7 42.0 + - - -
30H CYS 3.4 9.2 - - - +
31H ARG* 4.0 26.5 + - - +
36H GLY 4.0 0.6 + - - +
37H LEU* 1.3 75.4 - - - +
39H TYR* 1.3 73.3 + - - +
95H LEU* 3.6 23.2 + - + +
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Residues in contact with TYR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TYR* 3.8 15.5 - + - -
29H LYS* 3.7 3.3 - - - +
30H CYS* 2.9 41.3 + - - -
32H GLU* 3.4 34.6 + - + -
37H LEU* 3.3 37.6 - - + +
38H GLU* 1.3 78.0 - - - +
40H ALA* 1.3 59.9 + - - +
80H HIS* 3.1 45.6 - + + -
92H ILE* 3.9 11.7 - - + -
93H LEU 3.8 13.7 - - - +
94H GLU* 5.0 4.9 - - - -
95H LEU* 3.9 14.1 - - - +
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LEU* 5.0 0.7 - - + -
27H VAL* 4.4 15.0 - - + -
28H LYS 4.1 3.6 - - - -
29H LYS* 4.6 0.2 - - - +
30H CYS* 4.3 1.1 - - - -
39H TYR* 1.3 71.8 - - - +
41H ALA* 1.3 57.9 + - - +
42H LYS 4.0 0.2 - - - -
91H LEU 3.6 0.9 - - - +
92H ILE* 3.6 2.3 - - - -
93H LEU* 2.7 44.5 + - + +
94H GLU 3.7 16.2 - - - +
95H LEU* 3.4 23.0 - - + +
96H VAL 5.4 0.2 - - - +
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Residues in contact with ALA 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 5.6 1.6 - - + -
15H ILE* 5.2 2.7 - - + -
27H VAL* 3.3 2.6 - - - -
28H LYS 2.9 42.6 + - - +
30H CYS* 3.8 18.6 - - + -
40H ALA* 1.3 72.3 - - - +
42H LYS* 1.3 59.0 + - - +
43H PHE* 3.1 29.1 - - + -
90H VAL* 4.2 7.2 - - + -
91H LEU 3.3 7.0 - - - +
92H ILE* 4.6 5.6 - - + +
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Residues in contact with LYS 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ALA* 3.9 23.6 - - + -
26H ILE 3.8 2.5 - - - -
27H VAL* 3.8 22.9 - - + -
40H ALA 3.9 1.4 + - - -
41H ALA* 1.3 71.2 - - - +
43H PHE* 1.3 62.0 + - - +
44H ILE* 3.8 18.3 + - + -
64H GLU* 2.7 34.2 + - - +
89H VAL 3.2 2.4 - - - +
90H VAL* 3.2 4.2 - - - -
91H LEU* 2.7 54.6 + - + +
93H LEU* 4.5 17.4 - - + +
161H ASP* 5.2 8.1 + - - +
162H PHE 5.0 4.0 - - - +
163H GLY* 4.9 5.5 - - - +
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Residues in contact with PHE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 5.1 3.6 - - + -
10H GLU* 5.9 2.5 - - - -
15H ILE* 3.8 30.7 - - + -
24H PHE 3.6 0.2 - - - +
25H ALA* 2.8 3.8 - - - -
26H ILE* 2.8 62.5 + - + +
28H LYS* 4.1 23.3 - - + -
41H ALA* 3.1 30.1 - - + -
42H LYS* 1.3 70.4 - - - +
44H ILE* 1.3 62.3 + - - +
45H LYS 3.5 3.2 + - - -
88H ASP* 3.8 20.9 - - + +
89H VAL 3.6 3.4 - - - -
90H VAL* 3.5 33.2 - - + -
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Residues in contact with ILE 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PHE 3.4 3.6 - - - +
25H ALA* 3.7 17.3 - - + -
42H LYS* 4.0 13.0 - - + -
43H PHE* 1.3 71.5 - - - +
45H LYS* 1.3 62.0 + - - +
46H LYS 3.0 2.1 + - - -
56H VAL* 3.5 24.0 - - + -
61H ILE* 3.2 35.0 - - + -
64H GLU* 3.9 20.9 - - + +
65H VAL* 6.0 0.9 - - + -
88H ASP* 3.6 2.0 - - - -
89H VAL* 2.9 39.1 + - + +
91H LEU* 3.7 32.1 - - + -
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PHE* 2.5 27.5 + - + +
26H ILE* 6.5 1.6 - - - -
44H ILE* 1.3 67.9 - - - +
46H LYS* 1.3 75.4 + - - +
48H GLN* 5.6 8.1 - - - +
54H ARG* 5.4 4.7 - - + -
55H GLY* 3.1 9.7 - - - +
56H VAL* 2.9 20.3 + - - +
87H THR* 3.1 38.9 - - + +
88H ASP* 2.7 41.3 + - - +
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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