Contacts of the strand formed by residues 27 - 33 (chain B) in PDB entry 4NZD
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 THR 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A PRO* 6.0 5.8 - - + -
23B LEU* 3.9 5.8 - - - +
25B PRO 4.5 4.4 + - - -
26B SER* 1.3 76.6 + - - +
28B LEU* 1.3 74.7 + - - +
29B THR* 3.6 17.2 - - + +
78B GLN 3.3 1.6 - - - +
79B ILE* 3.3 7.8 - - - -
80B THR* 2.6 42.7 + - - -
81B ASP 5.4 1.8 - - - -
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Residues in contact with LEU 28 (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 LEU* 4.9 6.3 - - + -
16B CYS* 4.8 8.7 - - + -
18B LEU* 4.9 10.8 - - + -
23B LEU* 3.9 15.2 - - + +
27B THR* 1.3 78.6 - - - +
29B THR* 1.3 64.4 + - - +
48B LEU* 3.7 33.8 + - + +
60B TYR* 3.8 41.5 - - + -
77B VAL* 3.6 27.4 - - + -
78B GLN 3.6 7.4 - - - +
79B ILE* 3.7 22.0 - - + -
90B CYS* 5.2 0.4 - - - -
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Residues in contact with THR 29 (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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24A HIS* 5.5 11.7 - - + +
25A PRO* 6.3 2.2 - - + -
27B THR* 3.6 18.8 - - + +
28B LEU* 1.3 81.2 - - - +
30B LEU* 1.3 62.5 + - - +
31B THR* 5.3 2.9 - - - +
46B CYS 5.7 1.3 - - - -
48B LEU* 4.4 5.4 - - - -
77B VAL* 3.4 5.9 - - - +
78B GLN* 2.9 57.4 + - - +
80B THR* 5.0 7.8 + - - +
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Residues in contact with LEU 30 (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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14B VAL* 3.7 23.1 - - + -
16B CYS* 4.8 2.9 - - - -
29B THR* 1.3 76.3 - - - +
31B THR* 1.3 72.1 + - - +
32B TRP* 3.4 34.7 - - + +
43B ALA* 3.6 16.8 - - - +
46B CYS* 4.2 36.3 + - + +
48B LEU* 4.4 14.0 - - + +
75B PHE* 3.5 35.0 - - + -
76B SER 3.3 10.5 - - - +
77B VAL* 4.5 8.1 - - + -
78B GLN* 4.3 0.2 - - - -
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Residues in contact with THR 31 (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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29B THR* 5.3 2.7 - - - +
30B LEU* 1.3 83.7 - - - +
32B TRP* 1.3 61.7 + - - +
33B GLN* 2.9 23.1 + - - -
39B LEU* 3.9 18.3 - - + +
42B GLU 4.6 4.0 - - - -
43B ALA* 4.5 17.0 - - + +
75B PHE* 3.5 0.7 - - - -
76B SER 3.0 27.3 + - - -
78B GLN* 3.2 27.7 + - - +
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Residues in contact with TRP 32 (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 THR* 5.3 1.3 - - + -
14B VAL* 4.3 17.3 - - + -
30B LEU* 3.4 15.5 - - + +
31B THR* 1.3 73.4 - - - +
33B GLN* 1.3 65.3 + - - +
39B LEU* 3.6 7.8 - - - +
40B LYS* 2.8 35.1 + - + +
42B GLU* 3.9 14.4 + - + +
45B SER* 4.4 7.9 - - - -
46B CYS* 5.5 0.4 - - + -
64B MET* 3.2 35.5 - - + +
66B VAL* 4.0 26.7 - - + -
69B PHE* 3.4 31.4 - + + -
73B ASP* 4.5 5.6 - - + -
74B ILE 3.5 15.0 - - - -
75B PHE* 3.5 47.1 - + + -
95B LEU* 4.1 18.4 - - + -
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Residues in contact with GLN 33 (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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31B THR* 2.9 36.1 + - - -
32B TRP* 1.3 75.3 + - - +
34B ASP* 1.3 68.7 + - - +
37B GLU* 4.5 12.8 - - + +
38B GLU 3.7 5.8 - - - +
39B LEU* 3.5 30.2 - - + +
40B LYS* 3.7 11.7 - - - +
73B ASP* 3.6 11.1 - - - +
74B ILE* 2.5 48.4 + - + +
76B SER* 2.8 28.7 + - - -
78B GLN* 4.9 0.8 - - - +
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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