Contacts of the strand formed by residues 42 - 49 (chain A) in PDB entry 3NIE
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 GLY 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 3.4 3.8 - - - +
39A GLY 3.0 26.9 + - - +
41A TYR* 1.3 78.9 - - - +
43A TYR* 1.3 65.9 - - - -
44A VAL* 4.8 2.6 - - - +
59A LYS* 4.2 11.0 - - - -
60A LYS 3.3 11.7 - - - -
61A VAL* 4.4 1.6 - - - -
430A ANP 3.1 15.7 + - - +
262B THR* 4.3 0.6 - - - +
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.0 11.7 - - + -
37A GLY 3.6 1.6 - - - -
38A ARG* 3.0 30.0 + - + -
42A GLY* 1.3 75.6 - - - -
44A VAL* 1.3 61.2 + - - +
45A TYR* 3.5 25.3 - - + +
59A LYS* 3.5 0.3 - - - -
60A LYS* 2.8 32.9 + - + +
62A ASN* 5.9 2.9 - - - -
123B LYS 2.6 29.2 + - - -
124B THR 3.8 2.8 + - - -
125B PRO* 3.6 33.4 - - + -
260B ASN* 5.6 0.4 - - - -
261B PRO* 3.0 38.3 + - + -
262B THR* 3.5 23.8 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.4 3.3 - - - +
36A ILE* 3.0 28.0 + - + -
37A GLY 2.7 19.7 + - - +
38A ARG 4.5 0.2 - - - +
42A GLY 4.8 0.9 - - - +
43A TYR* 1.3 77.9 - - - +
45A TYR* 1.3 65.8 + - - +
57A ALA* 4.0 18.8 - - + -
58A ILE 3.2 9.2 - - - +
59A LYS* 3.8 19.1 - - + +
111A LEU* 6.1 0.2 - - + -
430A ANP 3.0 65.7 - - + +
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE* 3.8 18.6 - - + -
21A ILE* 5.0 1.8 - - - -
23A ASN* 3.4 23.0 + - - -
24A VAL* 3.5 34.3 - - + -
32A ILE* 4.4 15.5 - - + -
34A HIS 3.3 8.3 - - - +
35A LEU* 3.5 32.3 - - + -
36A ILE* 4.3 3.6 - - - +
43A TYR* 3.5 26.3 - - + +
44A VAL* 1.3 77.2 - - - +
46A LEU* 1.3 66.4 + - - +
47A ALA 3.6 0.5 + - - -
57A ALA* 3.4 6.4 - - - -
58A ILE* 2.9 47.4 + - + +
60A LYS* 4.4 10.8 - - + +
125B PRO* 3.6 15.6 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 3.7 3.8 - - - +
33A LYS* 2.8 58.5 + - + +
34A HIS* 2.7 43.3 + - + +
36A ILE* 3.5 22.0 - - + +
45A TYR* 1.3 72.8 - - - +
47A ALA* 1.3 61.7 + - - +
55A ASN* 3.7 29.2 - - + +
56A VAL 3.6 11.7 - - - +
113A ILE* 3.8 16.6 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TYR* 4.8 1.1 - - + -
31A GLU 3.1 17.5 - - - +
32A ILE* 3.6 9.6 - - + -
33A LYS* 4.1 1.1 - - - +
46A LEU* 1.3 77.8 - - - +
48A TYR* 1.3 60.2 + - - +
55A ASN* 3.5 7.6 - - - +
56A VAL* 2.8 38.8 + - + +
58A ILE* 3.4 34.8 - - + -
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN 3.4 3.6 - - - +
30A TYR* 3.5 2.8 - - - -
31A GLU* 2.9 60.0 + - + +
33A LYS* 4.6 11.0 - - + +
47A ALA* 1.3 73.6 - - - +
49A ASP* 1.3 70.5 + - - +
50A LYS* 3.8 10.6 + - + -
53A ASN* 3.4 27.6 + - - +
54A LYS* 3.7 21.8 - - - -
55A ASN* 3.6 20.0 - - - +
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Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 2.7 33.7 + - - -
30A TYR* 3.8 17.0 + - + -
47A ALA 4.1 0.6 + - - -
48A TYR* 1.3 72.8 - - - +
50A LYS* 1.3 57.2 + - - +
51A ASN* 3.1 10.4 + - - +
52A ALA* 3.1 19.2 + - + +
53A ASN* 2.9 28.2 + - - -
54A LYS 2.8 22.3 + - - +
56A VAL* 4.5 9.0 - - + -
93A HIS* 3.0 25.8 + - - -
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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