Contacts of the strand formed by residues 24 - 29 (chain A) in PDB entry 1QN7
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 24 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL 3.4 5.3 + - - -
23A PRO* 1.3 71.9 - - - +
25A LEU* 1.3 74.9 + - - +
26A GLN* 3.4 23.8 + - - +
120A GLY* 2.9 5.4 - - - -
121A SER 2.8 37.4 + - - -
122A CYS* 5.9 0.2 - - - +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO 4.3 6.7 - - - +
24A THR* 1.3 89.0 - - - +
26A GLN* 1.3 60.4 + - - +
27A ASN 3.9 0.2 - - - -
28A ILE* 4.2 8.1 - - + -
85A LYS* 3.3 33.3 - - - +
87A GLU* 3.5 27.6 - - - +
118A ILE* 3.9 25.1 - - + -
119A VAL 3.6 2.2 - - - -
120A GLY* 4.6 0.9 - - - -
178A ARG* 3.5 26.9 - - + +
181A THR* 4.3 20.6 - - + -
182A TYR* 4.5 13.5 - - + +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 3.4 32.6 - - - +
25A LEU* 1.3 74.1 - - - +
27A ASN* 1.3 60.9 + - + +
83A GLY 4.4 0.3 - - - +
84A ALA 4.0 0.8 - - - +
85A LYS* 2.6 48.3 + - - +
119A VAL* 2.7 17.4 + - + +
120A GLY* 4.4 0.9 - - - -
121A SER* 3.0 30.2 + - - +
223D T 3.5 8.6 - - - +
224D A 3.4 45.7 + - - +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU 3.9 0.8 - - - -
26A GLN* 1.3 79.7 - - - +
28A ILE* 1.3 68.0 + - - +
29A VAL* 4.2 4.4 - - - +
83A GLY* 2.7 36.5 + - - -
84A ALA 3.3 5.3 + - - -
118A ILE 3.6 0.2 - - - -
119A VAL* 2.7 40.7 + - + +
222D A 3.0 33.2 + - - -
223D T 3.2 43.8 + - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.2 10.5 - - + -
27A ASN* 1.3 87.2 + - - +
29A VAL* 1.3 66.6 + - - +
81A CYS 3.6 1.7 - - - +
82A THR* 3.5 4.9 - - - -
83A GLY 3.4 19.1 + - - -
84A ALA 2.9 20.5 + - - +
85A LYS 3.9 18.4 - - - +
86A SER* 3.9 17.7 - - - +
87A GLU* 4.1 4.5 - - + +
90A SER* 3.3 33.6 + - - +
115A ILE* 3.9 19.3 - - + -
117A ASN 3.4 3.8 - - - +
118A ILE* 4.0 31.6 - - + -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASN* 4.2 5.6 - - - +
28A ILE* 1.3 77.0 - - - +
30A SER* 1.3 61.4 + - - +
80A VAL* 4.2 7.2 - - + -
81A CYS 3.2 8.3 - - - +
82A THR* 4.1 4.7 - - + -
115A ILE* 3.6 2.4 - - - -
116A GLN* 2.7 42.0 + - + -
117A ASN* 2.8 24.1 + - + +
207C T 3.2 24.2 - - - +
208C A 3.7 29.2 - - + +
222D A 3.6 22.0 - - + +
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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