Contacts of the strand formed by residues 121 - 128 (chain F) in PDB entry 1NQ3
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 VAL 121 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F LEU* 3.7 21.5 - - - +
38F GLY 4.3 1.9 + - - -
51F VAL* 4.0 14.1 - - + +
54F GLU* 3.9 15.4 - - + +
55F ALA* 3.8 29.6 - - + +
58F ALA* 5.1 2.1 - - + +
81F VAL* 4.1 13.7 - - + -
82F LEU 3.2 12.6 - - - +
83F LEU* 4.0 14.4 - - + -
92F VAL* 4.4 10.1 - - + -
115F LEU* 3.5 4.2 - - - +
119F GLY 3.4 1.2 - - - -
120F ARG* 1.3 83.8 + - - +
122F GLU* 1.3 65.7 + - - +
123F ILE* 4.2 13.5 - - + -
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Residues in contact with GLU 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ALA* 4.2 16.5 - - - +
109E ALA 4.0 8.5 + - - +
110E TYR* 4.6 0.6 - - - -
35F GLY* 3.4 26.9 - - - +
36F GLN 3.4 18.8 - - - +
37F LEU* 3.6 10.8 - - + +
80F THR 3.7 0.7 - - - +
82F LEU* 2.8 49.0 + - + +
115F LEU* 3.6 19.7 - - + +
116F PRO* 3.5 28.2 - - - +
121F VAL* 1.3 76.4 - - - +
123F ILE* 1.3 67.7 + - - +
124F GLU* 4.3 0.8 - - + +
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Residues in contact with ILE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F SER 4.0 0.3 - - - +
35F GLY* 4.1 0.9 - - - -
36F GLN* 2.8 35.8 + - - +
55F ALA* 4.8 2.9 - - - +
58F ALA* 4.5 13.0 - - + -
59F LEU* 3.8 34.5 - - + -
62F ILE* 3.7 27.2 - - + +
79F ALA* 4.9 8.3 - - + -
80F THR 3.4 10.8 - - - +
81F VAL* 4.4 18.6 - - + -
82F LEU* 6.2 0.2 - - - -
92F VAL* 5.1 5.4 - - + -
96F TYR* 4.9 8.5 - - + -
100F PHE* 6.0 1.6 - - + -
121F VAL* 4.2 17.0 - - + -
122F GLU* 1.3 80.3 - - - +
124F GLU* 1.3 69.5 + - - +
125F ALA* 5.3 0.9 - - + -
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Residues in contact with GLU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LYS* 3.0 32.8 + - - +
80E THR* 4.7 3.3 + - - +
108E ALA* 3.6 15.2 - - - +
110E TYR* 4.3 8.5 + - - -
33F ILE 4.1 8.3 - - - +
34F SER 4.4 0.7 - - - -
35F GLY* 3.8 18.2 - - - +
62F ILE* 5.0 0.9 - - - -
79F ALA* 3.4 2.3 - - - +
80F THR* 2.9 60.3 + - - +
82F LEU* 4.1 17.6 - - + +
122F GLU* 5.7 0.2 - - - +
123F ILE* 1.3 76.2 - - - +
125F ALA* 1.3 65.4 + - - +
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Residues in contact with ALA 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 3.0 49.0 + - + +
62F ILE* 4.8 14.3 - - + +
76F VAL* 4.0 18.4 - - + -
78F LYS 3.3 12.6 - - - +
79F ALA* 4.2 5.6 - - + +
100F PHE* 5.7 2.2 - - + -
123F ILE* 5.3 0.7 - - + -
124F GLU* 1.3 79.6 - - - +
126F ILE* 1.3 68.6 + - - +
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Residues in contact with ILE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D TYR* 4.0 29.8 - - + +
126D ILE* 5.9 2.7 - - + -
78E LYS* 5.7 7.4 - - - +
126E ILE* 5.8 2.9 - - + -
30F THR* 3.7 27.6 - - + -
31F ILE 3.4 6.3 - - - +
32F TYR* 4.2 25.8 - - + -
76F VAL* 3.5 4.7 - - - +
77F VAL* 2.9 30.8 + - + +
78F LYS* 2.9 32.2 + - + +
125F ALA* 1.3 80.5 - - - +
127F ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F THR* 3.6 2.6 - - - +
31F ILE* 2.7 45.7 + - + +
33F ILE* 4.9 2.4 - - + +
66F LEU* 3.7 28.0 - - + -
75F ASN* 3.1 24.0 - - + +
76F VAL* 3.9 3.8 - - + -
77F VAL 4.2 1.1 - - - +
126F ILE* 1.3 75.9 - - - +
128F VAL* 1.3 67.6 + - - +
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Residues in contact with VAL 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.9 18.4 - - + -
27D VAL* 3.7 40.2 - - + -
32D TYR* 5.4 1.3 - - + -
29F ARG* 3.3 12.8 - - + +
30F THR* 4.3 16.8 - - + +
71F CYS* 4.7 0.9 - - - -
75F ASN* 2.9 28.2 + - - +
77F VAL* 4.1 17.3 - - + -
126F ILE* 5.4 0.2 - - + -
127F ALA* 1.3 79.7 - - - +
129F GLN* 1.3 75.2 + - - +
132F LEU* 3.7 12.2 - - + +
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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