Contacts of the strand formed by residues 44 - 47 (chain B) in PDB entry 2QN4
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 LEU 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B MET* 3.2 7.3 - - - -
35B ALA 2.9 29.6 + - - -
37B ARG* 3.6 39.3 - - + +
42B PRO* 3.5 19.5 - - + +
43B LEU* 1.3 75.6 - - - +
45B VAL* 1.3 63.9 + - - +
108B ARG* 3.5 40.2 - - + +
109B VAL 3.5 11.0 - - - +
110B VAL* 4.1 14.6 - - + +
157B TRP* 3.6 17.4 - - + -
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Residues in contact with VAL 45 (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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32B LEU* 4.4 5.4 - - + -
33B THR 3.5 9.9 - - - +
34B MET* 4.7 0.2 - - - +
44B LEU* 1.3 72.9 - - - +
46B ALA* 1.3 66.1 + - - +
84B PHE* 4.1 10.1 - - + -
96B TRP* 3.8 35.9 - - + +
109B VAL* 2.8 44.6 + - + +
111B THR* 4.4 6.5 - - + -
157B TRP* 3.7 7.7 - - - +
158B LEU* 2.9 50.2 + - + +
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Residues in contact with ALA 46 (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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32B LEU* 3.4 10.7 - - - +
33B THR* 2.8 43.7 + - + +
35B ALA* 4.3 9.9 - - + -
44B LEU 3.5 0.6 + - - -
45B VAL* 1.3 74.3 - - - +
47B GLN* 1.3 64.5 + - - +
155B ARG* 4.7 7.9 - - - -
156B ALA 3.1 14.1 - - - +
157B TRP* 3.7 22.0 - - + +
158B LEU 4.8 1.8 - - - -
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Residues in contact with GLN 47 (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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23B PRO* 3.8 1.0 - - - +
28B HIS 2.8 28.0 + - - +
29B GLY* 3.5 1.9 - - - -
30B GLY 2.9 31.1 + - - +
31B GLY 3.5 4.5 - - - +
32B LEU* 4.0 13.7 - - + -
33B THR* 4.6 1.3 - - - -
46B ALA* 1.3 77.6 - - - +
48B GLU* 1.3 72.3 + - - +
49B THR* 3.4 4.9 + - - +
149B VAL* 3.4 35.4 - - + +
155B ARG* 6.1 0.3 - - - -
156B ALA* 2.8 27.4 + - + +
157B TRP* 4.9 0.4 - - - +
158B LEU 4.9 0.4 - - - +
165B HIS* 3.3 20.7 + - - -
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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