Contacts of the strand formed by residues 30 - 37 (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 THR 30 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D TYR* 4.4 8.7 + - - +
25F VAL 3.6 1.7 - - - +
26F LEU* 3.4 0.7 - - - +
27F VAL* 2.9 36.5 + - - +
28F ASP* 5.7 0.7 - - - +
29F ARG* 1.3 81.2 - - - +
31F ILE* 1.3 64.1 + - - +
32F TYR* 3.8 27.6 - - + +
126F ILE* 3.7 26.5 - - + -
127F ALA 3.6 4.9 - - - +
128F VAL* 4.3 12.0 - - + +
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 4.9 5.6 - - + -
24F ALA* 4.1 13.0 - - + -
25F VAL 3.4 9.2 - - - +
26F LEU* 3.5 26.2 - - + +
29F ARG 4.4 2.2 - - - +
30F THR* 1.3 73.2 - - - +
32F TYR* 1.3 62.3 + - - +
33F ILE* 3.7 23.2 + - + +
65F ILE* 5.7 1.1 - - + -
66F LEU* 5.2 3.1 - - + -
69F ALA* 3.6 28.7 - - + +
71F CYS* 3.7 24.0 - - + -
126F ILE* 3.4 7.3 - - - +
127F ALA* 2.7 43.6 + - + +
129F GLN* 4.6 7.9 - - + +
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Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 4.7 5.0 + - - -
30E THR* 4.4 11.6 + - - +
32E TYR* 4.6 6.8 + - - -
77E VAL* 4.0 21.3 - - + +
78E LYS* 4.1 26.2 - - + +
106E ALA* 3.4 17.1 - - + +
126E ILE* 3.8 34.1 - - + +
128E VAL* 5.5 1.9 - - + +
24F ALA* 3.1 4.0 - - - -
25F VAL 2.9 37.9 + - - +
27F VAL* 3.8 28.7 - - + -
30F THR* 3.8 23.1 - - + +
31F ILE* 1.3 71.7 - - - +
33F ILE* 1.3 61.1 + - - +
125F ALA 4.3 2.5 - - - -
126F ILE* 4.2 28.0 - - + -
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Residues in contact with ILE 33 (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* 5.0 8.0 + - - +
106E ALA* 4.3 2.5 - - - -
23F GLN 3.8 10.8 - - - +
24F ALA* 4.0 4.7 - - + -
31F ILE* 3.9 18.6 - - + +
32F TYR* 1.3 75.8 - - - +
34F SER* 1.3 77.0 + - - +
35F GLY 3.7 0.5 + - - -
36F GLN* 4.5 5.2 - - + +
62F ILE* 4.3 18.4 - - + -
65F ILE* 4.2 25.1 - - + -
66F LEU* 3.8 33.9 - - + -
76F VAL* 5.7 0.4 - - + -
124F GLU* 4.1 5.0 - - - +
125F ALA* 3.0 41.4 + - + +
127F ALA* 4.9 4.5 - - + -
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Residues in contact with SER 34 (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* 5.8 0.7 - - - -
106E ALA* 3.4 3.2 - - - +
107E ARG 2.8 33.2 + - - +
21F TYR* 3.8 12.7 - - - -
22F SER 2.5 25.6 + - - -
23F GLN* 2.9 18.6 + - - -
33F ILE* 1.3 82.8 - - - +
35F GLY* 1.3 69.4 + - - +
36F GLN* 3.2 18.6 + - - +
123F ILE 4.0 1.9 - - - +
124F GLU* 4.4 0.3 - - - -
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Residues in contact with GLY 35 (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* 6.0 0.2 - - - +
107E ARG 3.0 14.4 + - - +
108E ALA* 4.4 3.6 - - - +
21F TYR* 6.0 1.2 - - - -
33F ILE 3.7 1.0 + - - -
34F SER* 1.3 74.0 - - - +
36F GLN* 1.3 64.1 + - - +
37F LEU* 4.1 2.3 + - - +
122F GLU* 3.4 26.5 - - - +
123F ILE 3.5 8.7 - - - -
124F GLU* 3.8 14.5 - - - +
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Residues in contact with GLN 36 (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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14F ALA* 5.0 0.2 - - - +
15F PRO* 3.9 22.0 + - - +
21F TYR* 6.1 0.5 - - - -
23F GLN* 4.2 5.6 - - - +
33F ILE* 4.5 0.4 - - + -
34F SER* 3.3 26.7 - - - +
35F GLY* 1.3 76.3 - - - +
37F LEU* 1.3 62.4 + - - +
58F ALA* 3.8 16.4 - - - +
61F ASN* 3.7 18.2 + - + +
62F ILE* 3.6 28.0 - - + -
65F ILE* 3.5 27.6 - - + +
122F GLU* 3.4 5.5 - - - -
123F ILE 2.8 36.6 + - - +
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Residues in contact with LEU 37 (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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15F PRO* 5.4 0.6 - - - +
35F GLY 5.2 1.8 - - - +
36F GLN* 1.3 78.4 + - - +
38F GLY* 1.3 59.6 + - - +
39F MET* 2.8 42.7 + - + +
46F LEU* 4.4 4.5 - - + -
58F ALA* 3.5 9.0 - - - -
61F ASN* 3.3 14.6 - - - +
115F LEU* 4.4 10.1 - - + -
116F PRO* 4.0 40.4 - - + +
117F LYS* 5.1 3.4 - - + -
119F GLY* 4.5 7.4 - - - -
121F VAL 3.7 18.4 - - - +
122F GLU* 3.6 26.5 - - + +
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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