Contacts of the strand formed by residues 42 - 49 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A THR* 4.3 0.8 - - - +
38B ARG* 3.2 7.1 - - - +
39B GLY 3.1 24.1 + - - +
41B TYR* 1.3 80.3 - - - +
43B TYR* 1.3 66.1 + - - -
44B VAL* 4.0 5.3 + - - +
59B LYS* 4.2 14.4 - - - -
60B LYS 3.5 10.1 - - - -
61B VAL* 4.5 1.6 - - - -
430B ANP 3.0 10.7 + - - +
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS 2.6 30.1 + - - -
125A PRO* 3.8 24.7 - - + -
260A ASN* 5.3 0.7 - - - -
261A PRO* 3.4 30.3 - - + +
262A THR* 3.5 28.7 - - + -
35B LEU* 3.8 19.3 - - + -
37B GLY 3.6 1.1 - - - -
38B ARG* 2.9 38.5 + - + -
42B GLY* 1.3 73.0 - - - -
44B VAL* 1.3 59.6 + - - +
45B TYR* 3.3 28.0 - - + +
59B LYS* 3.6 0.2 - - - -
60B LYS* 3.0 33.5 + - + +
62B ASN* 5.7 7.0 - - - -
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Residues in contact with VAL 44 (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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35B LEU* 3.4 3.5 - - - +
36B ILE* 2.9 27.4 + - + +
37B GLY 2.7 17.0 + - - +
42B GLY 4.4 3.1 - - - +
43B TYR* 1.3 76.6 - - - +
45B TYR* 1.3 64.8 + - - +
57B ALA* 3.8 27.1 - - + -
58B ILE 3.5 9.4 - - - +
59B LYS* 3.7 23.8 - - + +
111B LEU* 5.7 0.7 - - + -
430B ANP 3.4 57.7 - - + +
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Residues in contact with TYR 45 (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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125A PRO* 3.5 25.4 - - + +
20B ILE* 4.4 10.8 - - + -
21B ILE* 4.3 12.8 - - + -
23B ASN* 3.6 13.7 + - - -
24B VAL* 3.5 32.1 - - + -
32B ILE* 4.6 10.1 - - + -
34B HIS 3.3 9.6 - - - +
35B LEU* 3.6 34.3 - - + -
36B ILE* 3.8 4.7 - - - -
43B TYR* 3.3 34.2 - - + +
44B VAL* 1.3 73.7 - - - +
46B LEU* 1.3 66.5 + - - +
47B ALA 3.5 0.7 + - - -
57B ALA* 3.4 4.0 - - - -
58B ILE* 3.0 42.6 + - + +
60B LYS* 4.5 10.3 - - + +
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Residues in contact with LEU 46 (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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32B ILE* 3.9 1.7 - - - -
33B LYS* 2.9 34.0 + - + -
34B HIS* 2.8 46.3 + - + +
36B ILE* 3.7 20.3 - - + +
45B TYR* 1.3 75.4 - - - +
47B ALA* 1.3 67.0 + - - +
55B ASN* 3.9 31.9 - - + +
56B VAL 3.7 2.2 - - - +
113B ILE* 3.5 26.9 - - + -
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Residues in contact with ALA 47 (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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30B TYR* 4.7 2.2 - - + -
31B GLU 3.2 17.3 - - - +
32B ILE* 3.8 10.3 - - + -
33B LYS* 4.3 1.6 - - - +
45B TYR* 4.7 0.4 - - + +
46B LEU* 1.3 78.1 - - - +
48B TYR* 1.3 59.0 + - - +
55B ASN* 3.3 7.7 - - - +
56B VAL* 2.8 40.1 + - + +
58B ILE* 3.5 34.5 - - + -
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Residues in contact with TYR 48 (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 ASN 3.4 5.2 - - - +
30B TYR* 3.6 1.7 - - - -
31B GLU* 3.0 49.0 + - + +
33B LYS* 4.8 7.9 - - + +
47B ALA* 1.3 72.7 - - - +
49B ASP* 1.3 57.3 + - - +
50B LYS* 3.5 28.7 + - + -
53B ASN* 3.1 30.8 + - - +
54B LYS 3.2 30.5 - - - -
55B ASN* 3.6 16.4 - - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASN* 2.8 29.5 + - - -
30B TYR* 3.7 20.5 + - + -
47B ALA 3.9 2.2 + - - -
48B TYR* 1.3 70.7 - - - +
50B LYS* 1.3 57.9 + - - +
51B ASN* 3.2 10.6 + - - +
52B ALA* 3.4 15.7 + - + +
53B ASN* 2.9 23.7 + - - -
54B LYS 2.6 22.5 + - - +
56B VAL* 4.2 8.9 - - + +
93B HIS* 2.7 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