Contacts of the helix formed by residues 109 - 116 (chain D) in PDB entry 1QSW
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 TRP 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D TRP* 4.6 5.2 - + - -
31D LEU* 3.7 33.7 - - + -
35D GLU* 3.3 26.9 - - - +
57D PHE* 2.8 29.3 + - + -
58D GLN* 3.2 13.5 + - + -
59D ILE* 4.3 17.0 - - + +
96D ALA* 4.6 7.2 - - + -
99D VAL* 3.7 32.5 - - + -
100D VAL* 3.7 27.6 - - + -
105D GLY 4.4 1.6 - - - -
106D ILE* 3.2 26.4 + - + +
107D ARG 3.1 7.9 - - - +
108D ALA* 1.3 80.4 - - + +
110D VAL* 1.3 65.0 + - - +
112D TRP* 3.1 13.1 + - + +
113D ARG* 3.3 9.0 + - - +
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLU* 4.7 0.6 + - - -
108D ALA 3.9 3.8 + - - +
109D TRP* 1.3 68.5 - - - +
111D ALA* 1.3 57.3 + - - +
113D ARG* 3.2 41.0 + - - +
114D ASN* 2.7 59.5 + - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 5.2 1.1 - - + -
34D TRP* 4.2 22.9 - - + +
35D GLU* 3.0 31.7 + - + +
109D TRP 3.2 0.4 - - - -
110D VAL* 1.3 83.2 - - - +
112D TRP* 1.3 52.6 + - - +
114D ASN* 3.7 3.8 - - - +
115D ARG* 2.7 43.1 + - - +
116D CYS* 5.1 1.1 - - - -
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Residues in contact with TRP 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN* 2.9 44.5 + - - -
31D LEU* 4.2 19.2 - - + +
35D GLU* 4.4 0.2 + - - -
106D ILE* 3.3 61.4 - - + +
107D ARG* 4.2 21.5 - - + -
109D TRP* 3.1 11.7 + - - +
111D ALA* 1.3 80.6 - - - +
113D ARG* 1.3 64.3 + - + +
116D CYS* 2.7 54.0 + - + +
117D GLN* 2.8 58.3 + - + -
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLN* 4.9 6.2 - - - +
107D ARG* 2.9 39.6 + - + +
108D ALA 5.3 1.6 + - - -
109D TRP 3.3 5.8 + - - +
110D VAL* 3.2 41.1 + - - +
112D TRP* 1.3 94.4 - - + +
114D ASN* 1.3 70.1 + - - +
117D GLN* 3.8 31.2 + - - +
119D ARG* 5.4 0.2 + - - -
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Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D VAL* 2.7 46.2 + - - +
111D ALA* 4.1 2.7 - - - +
113D ARG* 1.3 85.0 + - - +
115D ARG* 1.3 80.3 + - - +
119D ARG* 2.8 30.8 + - - -
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 3.7 8.1 - - - -
34D TRP* 3.3 67.0 + - + -
111D ALA* 2.7 23.1 + - - +
114D ASN* 1.3 96.1 - - - +
116D CYS* 1.3 59.3 + - - +
119D ARG* 3.3 25.7 + - - +
121D VAL* 5.1 0.3 - - - +
124D TYR* 4.9 1.9 + - - -
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Residues in contact with CYS 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN* 4.1 6.0 - - - +
30D CYS* 2.0 62.1 - - + -
31D LEU* 3.9 1.1 - - - -
34D TRP* 4.1 4.9 - - - -
111D ALA 4.5 0.4 - - - -
112D TRP* 2.7 48.7 + - + +
114D ASN 3.7 0.2 - - - -
115D ARG* 1.3 77.6 - - - +
117D GLN* 1.3 68.0 + - - +
118D ASN 3.3 0.5 + - - -
119D ARG* 3.0 15.8 + - - +
121D VAL* 3.6 14.9 - - + +
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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