Contacts of the strand formed by residues 51 - 58 (chain B) in PDB entry 3NGA
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 SER 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ARG* 3.2 12.8 + - - +
48B GLY* 2.7 36.0 + - - -
49B LYS 3.7 1.8 - - - -
50B TYR* 1.4 82.1 - - - +
52B GLU* 1.3 57.8 + - - +
53B VAL* 4.3 7.3 - - - +
68B LYS* 3.7 37.0 - - - +
69B ILE 3.3 15.7 - - - -
70B LEU* 4.3 1.6 - - - -
71B LYS* 4.1 5.4 - - - -
175B ASP* 5.7 0.2 + - - -
1000B 3NG 5.7 0.9 - - - +
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Residues in contact with GLU 52 (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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44B LYS* 2.8 33.8 + - + -
46B GLY 3.5 7.4 - - - +
47B ARG* 3.6 28.1 - - + -
51B SER* 1.3 72.7 - - - +
53B VAL* 1.3 62.6 + - - +
54B PHE* 3.7 24.0 - - + -
67B VAL 3.6 1.0 - - - +
68B LYS* 3.5 2.1 - - - -
69B ILE* 3.0 40.7 + - + +
71B LYS* 4.0 24.3 + - - +
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Residues in contact with VAL 53 (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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44B LYS* 3.6 5.4 - - - +
45B LEU* 2.7 37.4 + - + -
46B GLY 2.8 15.6 + - - +
51B SER* 4.3 5.8 - - - +
52B GLU* 1.3 76.1 - - - +
54B PHE* 1.3 59.4 + - - +
66B VAL* 3.3 30.5 - - + -
67B VAL 3.5 2.0 - - - +
68B LYS* 4.0 23.3 - - + -
1000B 3NG 3.6 53.6 - - + +
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Residues in contact with PHE 54 (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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41B LEU* 3.9 37.9 - - + -
43B ARG 3.3 10.1 - - - +
44B LYS* 3.6 44.9 - - + -
45B LEU* 4.2 6.3 - - - +
52B GLU* 3.7 31.9 - - + -
53B VAL* 1.3 75.3 - - - +
55B GLU* 1.3 62.3 + - - +
66B VAL* 3.3 5.0 - - - +
67B VAL 2.8 42.8 + - - +
69B ILE* 3.5 32.1 - - + -
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Residues in contact with GLU 55 (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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41B LEU* 3.7 1.9 - - - -
42B VAL* 2.7 47.1 + - + +
43B ARG* 2.8 50.2 + - + +
45B LEU* 3.8 20.3 - - + +
54B PHE* 1.3 74.1 - - - +
56B ALA* 1.3 56.9 + - - +
64B LYS* 3.6 42.1 + - + +
65B VAL 3.7 5.6 - - - +
66B VAL* 4.6 1.3 - - + -
115B HIS* 4.1 14.7 - - + -
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Residues in contact with ALA 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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39B TYR* 4.5 5.2 - - + -
40B GLN 3.2 19.5 - - - +
41B LEU* 4.0 6.7 - - + -
42B VAL* 4.0 7.6 - - - +
54B PHE 3.7 0.2 + - - -
55B GLU* 1.3 74.8 - - - +
57B ILE* 1.3 61.7 + - - +
64B LYS* 3.5 10.0 - - - +
65B VAL* 2.8 37.0 + - + +
67B VAL* 3.6 30.5 - - + -
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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
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39B TYR* 3.4 4.8 - - - -
40B GLN* 2.9 61.3 + - + +
42B VAL* 4.2 14.1 - - + -
56B ALA* 1.3 73.8 - - - +
58B ASN* 1.3 75.5 + - - +
59B ILE* 3.3 5.7 + - + +
62B ASN* 3.3 40.8 - - + +
63B GLU 3.4 6.5 - - - +
64B LYS* 4.7 5.4 - - + +
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Residues in contact with ASN 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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38B ASP* 3.4 13.0 + - - +
39B TYR* 3.6 36.0 + - + -
57B ILE* 1.3 69.4 - - - +
59B ILE* 1.3 56.3 + - - +
60B THR* 2.7 31.5 + - - +
61B ASN* 3.2 26.7 + - - +
62B ASN* 2.8 34.7 + - - -
63B GLU* 2.8 20.1 + - + +
65B VAL* 4.5 6.2 - - + +
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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