Contacts of the strand formed by residues 55 - 60 (chain B) in PDB entry 1NAP
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 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG 4.9 0.3 - - - +
25B CYS* 3.4 3.3 - - - +
26B LEU* 2.8 38.5 + - - +
27B CYS* 3.0 33.5 + - + +
43B GLU 3.7 1.0 - - - +
44B VAL* 3.6 2.3 - - - -
45B ILE* 2.8 52.0 + - + +
51B CYS* 3.9 10.1 - - + +
53B GLN* 2.7 36.6 + - - +
54B VAL* 1.3 80.1 - - - +
56B VAL* 1.3 64.5 + - - +
57B ILE* 4.2 2.2 - - + -
70B PRO* 5.0 1.3 - - - -
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Residues in contact with VAL 56 (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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83A LEU* 3.8 18.4 - - + -
27B CYS* 4.6 1.5 - - - -
42B LEU* 4.0 24.9 - - + -
43B GLU 3.4 8.5 - - - +
44B VAL* 4.6 9.9 - - + -
54B VAL* 4.5 2.5 - - + -
55B GLU* 1.3 78.3 - - - +
57B ILE* 1.3 61.8 + - - +
58B ALA 4.1 0.2 - - - -
67B CYS* 3.4 4.9 - - - +
68B LEU* 2.6 54.8 + - + +
70B PRO* 3.7 32.3 - - + -
75B ILE* 4.8 7.4 - - + -
79B VAL* 4.8 4.7 - - + -
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.5 35.2 - - + -
27B CYS* 3.9 17.0 - - - -
42B LEU* 3.5 1.9 - - - -
43B GLU* 2.9 48.3 + - + +
45B ILE* 4.1 14.4 - - + -
55B GLU* 5.0 1.8 - - + +
56B VAL* 1.3 79.5 - - - +
58B ALA* 1.3 63.9 + - - +
59B THR* 4.0 3.2 + - - +
65B LYS* 3.9 36.8 - - + +
66B ILE 3.4 4.9 - - - +
67B CYS* 4.4 3.6 - - - -
23D LEU* 3.8 15.0 - - + -
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Residues in contact with ALA 58 (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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34B ILE* 5.4 0.4 - - + -
39B ILE* 4.3 16.2 - - + -
41B SER 3.3 7.0 - - - +
42B LEU* 3.9 10.1 - - + -
56B VAL 4.1 0.8 - - - -
57B ILE* 1.3 75.9 - - - +
59B THR* 1.3 61.5 + - - +
60B LEU* 3.9 9.3 + - + +
64B ARG 3.7 0.5 - - - +
65B LYS* 3.3 5.0 - - - +
66B ILE 2.8 34.6 + - - +
68B LEU* 3.9 28.9 - - + +
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Residues in contact with THR 59 (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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39B ILE* 3.8 1.4 - - - -
40B GLN* 2.8 53.4 + - - +
41B SER* 2.8 28.7 + - - +
57B ILE* 4.0 3.1 + - - +
58B ALA* 1.3 73.4 - - - +
60B LEU* 1.3 60.6 + - - +
63B GLY* 4.2 13.0 - - - +
64B ARG 3.5 5.2 - - - +
65B LYS* 2.5 36.6 + - - +
40C GLN* 4.1 10.1 - - - +
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Residues in contact with LEU 60 (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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34B ILE* 4.3 20.9 - - + -
38B ASN* 3.0 28.0 - - + +
39B ILE* 4.9 1.8 - - + -
40B GLN* 3.9 6.1 - - - +
58B ALA* 4.0 16.6 - - + +
59B THR* 1.3 84.0 - - - +
61B LYS* 1.3 61.5 + - - +
62B ASP* 3.0 15.3 - - - +
63B GLY* 2.9 19.9 + - - -
64B ARG* 2.8 41.6 + - - +
66B ILE* 3.5 34.8 - - + -
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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