Contacts of the strand formed by residues 106 - 111 (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 ALA 106 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D SER 3.7 7.0 - - - +
25D VAL* 3.8 8.6 - - - +
32D TYR* 3.3 26.7 - - + +
34D SER* 3.3 19.3 - - - +
77F VAL 3.0 16.5 + - - +
78F LYS* 4.0 15.5 - - + -
79F ALA* 3.0 21.8 + - - +
105F PRO* 1.3 78.0 - - - +
107F ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 107 (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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18D ILE 5.1 1.6 + - - -
20D PRO* 4.0 4.0 - - - +
21D TYR* 3.5 50.3 - - + +
22D SER 4.4 0.2 + - - -
34D SER* 2.7 18.6 + - - +
35D GLY* 3.0 22.3 + - - +
78F LYS* 4.4 2.9 - - - +
79F ALA 3.2 13.5 - - - +
81F VAL* 4.2 13.3 - - + +
89F PHE* 3.6 26.9 - - - -
93F ASN* 3.0 29.5 + - - +
96F TYR* 3.6 44.8 - - - +
105F PRO 4.4 0.7 - - - +
106F ALA* 1.3 78.7 - - - +
108F ALA* 1.3 80.6 + - - +
109F ALA* 4.9 3.8 - - - +
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Residues in contact with ALA 108 (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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35D GLY 4.3 4.7 - - - +
122D GLU* 4.2 15.0 - - - +
124D GLU* 3.8 33.0 - - - +
78F LYS* 4.4 5.4 - - - -
79F ALA 3.2 4.3 + - - +
80F THR* 3.3 8.2 - - + +
81F VAL 2.9 23.9 + - - -
107F ARG* 1.3 78.9 - - - +
109F ALA* 1.3 61.9 + - - +
110F TYR* 4.4 10.3 - - + -
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Residues in contact with ALA 109 (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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116D PRO* 3.4 24.8 - - + +
122D GLU* 3.7 7.3 + - - +
81F VAL* 3.3 22.7 - - + +
83F LEU* 5.2 2.0 - - + -
86F ILE* 5.2 0.9 - - + -
89F PHE* 3.9 32.5 - - + -
107F ARG* 4.6 6.0 - - - +
108F ALA* 1.3 75.4 - - - +
110F TYR* 1.3 69.7 + - - +
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Residues in contact with TYR 110 (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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82D LEU* 3.4 30.5 - - + +
110D TYR* 3.7 17.1 + + - -
112D VAL* 3.7 29.8 - - + -
114D ALA 3.6 11.9 - - - +
115D LEU* 3.8 14.8 - - + -
116D PRO* 4.7 0.2 - - - -
122D GLU* 4.8 1.6 - - - -
124D GLU* 4.2 10.0 + - - -
110E TYR* 3.8 7.5 + - - -
80F THR* 4.0 20.5 - - + +
81F VAL 3.2 6.4 + - - +
82F LEU* 3.6 28.6 - - + +
83F LEU* 3.0 26.6 + - - +
86F ILE* 4.2 11.2 - - - +
108F ALA* 4.4 4.3 - - + -
109F ALA* 1.3 85.2 - - - +
111F GLN* 1.3 64.5 + - - +
112F VAL* 4.0 8.7 - - + -
124F GLU* 5.4 0.2 + - - -
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Residues in contact with GLN 111 (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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112D VAL* 3.4 10.2 - - - +
113D ALA* 2.9 41.7 + - - +
114D ALA* 2.9 29.1 + - + +
83F LEU* 3.1 15.9 - - - +
84F ALA 3.3 25.3 + - - +
85F ASP* 3.7 4.0 - - - +
86F ILE* 2.9 37.4 + - + +
110F TYR* 1.3 72.3 - - - +
112F VAL* 1.3 64.8 + - - +
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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