Contacts of the helix formed by residues 55 - 62 (chain A) in PDB entry 1QFG
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 1.3 74.1 - - - +
56A GLU* 1.3 64.5 + - - +
58A MET* 3.1 12.6 + - - +
59A ALA* 2.8 36.6 + - - +
126A LEU 4.1 5.6 - - - +
127A GLU* 3.0 37.8 + - + +
154A LYS* 5.3 6.5 - - - -
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Residues in contact with GLU 56 (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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21A ALA* 3.9 42.3 - - + +
22A TRP* 4.0 11.5 - - - +
25A ALA* 5.3 1.8 - - + +
26A ALA* 4.5 8.1 - - + -
29A ALA* 5.3 5.0 - - - +
54A THR* 3.5 20.5 + - - +
55A ALA* 1.3 85.6 + - - +
57A GLU* 1.3 60.2 + - - +
59A ALA* 3.2 9.5 + - - +
60A LEU* 2.9 28.1 + - - +
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Residues in contact with GLU 57 (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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22A TRP* 4.5 11.7 - - + +
26A ALA* 4.2 16.4 - - + +
52A VAL 4.0 4.3 - - - +
53A VAL* 3.9 19.5 - - + +
54A THR* 2.6 50.8 + - - +
56A GLU* 1.3 77.4 - - - +
58A MET* 1.3 61.6 + - - +
60A LEU* 3.0 5.4 + - - +
61A HIS* 3.0 37.2 + - + +
586A LYS* 4.1 20.8 + - - -
596A VAL* 5.0 6.9 - - - +
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Residues in contact with MET 58 (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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53A VAL* 4.2 16.8 - - + +
54A THR 3.0 13.6 + - - +
55A ALA* 3.1 19.3 + - - +
57A GLU* 1.3 77.0 - - - +
59A ALA* 1.3 57.7 + - - +
61A HIS* 4.8 0.9 - - - -
62A GLN* 2.8 31.4 + - - -
63A PRO* 3.4 16.9 - - + +
66A VAL* 5.8 0.9 - - - -
69A ALA* 4.1 24.7 - - + -
123A PRO* 4.3 24.5 - - + +
126A LEU* 4.0 22.9 - - + +
127A GLU 4.2 0.4 - - - -
128A ARG* 3.9 31.2 - - - +
129A ALA* 5.1 5.2 - - + -
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Residues in contact with ALA 59 (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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55A ALA 2.8 16.8 + - - +
56A GLU* 3.4 11.0 - - - +
57A GLU 3.1 0.2 - - - -
58A MET* 1.3 76.4 - - - +
60A LEU* 1.3 60.6 + - - +
62A GLN* 2.8 25.2 + - - +
674A ARG* 3.6 20.3 + - - +
690A HIS* 5.2 0.3 + - - -
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Residues in contact with LEU 60 (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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22A TRP* 3.4 48.4 - - + +
56A GLU 2.9 13.2 + - - +
57A GLU* 3.0 8.0 + - - +
59A ALA* 1.3 80.3 - - - +
61A HIS* 1.3 63.8 + - + +
628A TRP* 3.1 36.8 - - + -
642A THR* 4.7 3.1 - - + -
672A LEU* 3.3 31.3 - - + +
674A ARG* 3.9 25.5 + - - +
690A HIS* 2.9 25.5 + - - -
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Residues in contact with HIS 61 (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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57A GLU* 3.0 28.5 + - + +
58A MET* 4.8 0.4 - - - -
60A LEU* 1.3 82.6 - - + +
62A GLN* 1.3 71.9 + - - +
63A PRO* 3.5 10.6 - - + +
72A TYR* 3.9 21.5 - + - -
596A VAL* 5.3 4.5 - - + -
628A TRP* 3.0 65.0 + + + -
672A LEU* 4.4 5.8 - - + +
690A HIS* 3.8 10.6 + - - -
692A ASN* 5.6 2.6 - - - +
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Residues in contact with GLN 62 (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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58A MET 2.8 27.1 + - - -
59A ALA* 2.8 29.7 + - - +
61A HIS* 1.3 73.2 - - - +
63A PRO* 1.4 70.3 - - - +
64A LYS* 3.6 1.6 + - - -
165A GLN* 4.2 19.8 + - - +
167A LYS* 2.5 38.9 + - - +
690A HIS* 3.0 38.4 - - + +
692A ASN* 5.7 2.9 + - - -
720A THR* 4.5 5.2 - - - +
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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