Contacts of the helix formed by residues 107 - 116 (chain A) in PDB entry 1QXP
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASP 4.4 6.5 - - - +
105A SER 2.7 2.8 + - - -
106A TRP* 1.3 111.5 - - + +
108A LEU* 1.3 58.4 + - - +
110A ALA* 2.8 27.2 + - - +
111A ILE* 3.2 24.7 + - + +
168A VAL* 4.9 4.9 - - + -
182A GLU* 4.2 31.2 - - + +
185A TYR* 4.2 22.0 - - + -
195A LEU* 4.7 9.4 - - + -
200A THR* 5.2 0.2 - - - -
203A ALA* 4.4 3.8 - - + -
207A PHE* 4.4 16.6 - - + -
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Residues in contact with LEU 108 (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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97A ILE* 3.3 41.7 - - + -
98A CYS* 3.6 13.2 - - - +
99A GLN* 3.1 42.4 - - + +
104A ASP 4.9 0.2 + - - -
105A SER* 2.6 26.5 + - - +
107A LEU* 1.3 75.4 - - - +
109A ALA* 1.3 58.5 + - + +
111A ILE* 3.5 4.5 + - - +
112A ALA* 2.7 33.8 + - - +
168A VAL* 4.9 7.4 - - + +
262A HIS* 4.6 16.4 - - + +
288A TRP* 4.1 13.7 - - + -
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Residues in contact with ALA 109 (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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105A SER 4.9 0.2 - - - +
106A TRP 2.7 17.9 + - - +
108A LEU* 1.3 80.4 - - + +
110A ALA* 1.4 52.4 + - - +
112A ALA* 3.8 4.3 - - - +
113A SER* 2.6 40.0 + - - +
200A THR* 4.3 13.0 - - + -
204A PHE* 5.3 1.8 - - - -
262A HIS* 2.9 31.9 - - - +
263A ALA* 4.8 4.9 - - + +
288A TRP* 4.6 2.0 - - - -
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Residues in contact with ALA 110 (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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106A TRP 4.2 1.2 + - - -
107A LEU* 2.8 16.6 + - - +
109A ALA* 1.4 73.0 - - - +
111A ILE* 1.3 59.2 - - - +
113A SER* 3.4 10.2 + - - -
114A LEU* 3.8 14.7 + - - +
200A THR* 4.6 8.0 - - - +
203A ALA* 3.6 30.3 - - + -
204A PHE* 4.4 21.1 - - - +
207A PHE* 3.9 15.6 - - + -
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Residues in contact with ILE 111 (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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97A ILE* 3.3 21.1 - - + -
107A LEU* 3.2 28.4 + - + +
108A LEU 3.7 7.0 - - - +
110A ALA* 1.3 73.7 - - - +
112A ALA* 1.3 71.5 + - - +
114A LEU* 3.3 23.3 + - - +
115A THR* 3.7 7.4 + - - -
168A VAL* 4.6 11.7 - - + -
177A TRP* 4.0 9.7 - - + -
178A SER* 3.9 32.8 - - - +
181A LEU* 4.5 13.9 - - + -
182A GLU* 4.6 9.2 - - + +
207A PHE* 4.0 18.4 - - + -
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Residues in contact with ALA 112 (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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95A THR* 4.8 7.0 + - + -
97A ILE* 4.1 15.7 - - + +
108A LEU 2.7 22.4 + - - +
109A ALA 3.8 3.4 - - - +
111A ILE* 1.3 74.7 - - - +
113A SER* 1.3 57.2 + - - +
114A LEU 2.7 12.6 + - - -
115A THR* 3.7 16.6 + - - -
116A LEU* 4.3 6.2 + - - +
287A PRO* 4.3 10.9 - - + +
288A TRP* 3.9 26.2 - - + -
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Residues in contact with SER 113 (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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109A ALA* 2.6 29.0 + - - +
110A ALA 3.4 3.1 + - - -
111A ILE 3.3 0.8 - - - -
112A ALA* 1.3 73.4 - - - +
114A LEU* 1.4 56.5 + - - +
116A LEU* 3.4 29.3 - - - +
117A ASN 4.9 1.0 + - - -
120A ILE* 5.9 0.3 - - - +
204A PHE* 3.6 34.8 - - - -
237A LEU* 4.8 6.6 - - - +
239A GLY* 6.1 0.5 - - - -
263A ALA* 5.1 7.8 - - - +
265A SER* 4.2 11.0 + - - -
287A PRO* 5.1 2.8 - - - +
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Residues in contact with LEU 114 (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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110A ALA 3.9 13.9 - - - +
111A ILE* 3.4 10.8 - - - +
112A ALA 2.7 5.3 + - - -
113A SER* 1.4 76.1 - - - +
115A THR* 1.4 53.2 - - - +
117A ASN 3.0 34.7 + - - +
120A ILE* 3.6 32.9 - - + +
121A LEU* 3.2 33.8 - - + +
124A VAL* 4.3 11.9 - - + -
177A TRP* 4.2 13.5 - - + -
181A LEU* 4.2 15.3 - - + -
204A PHE* 5.5 4.5 - - + -
207A PHE* 4.4 23.8 - - + +
208A THR* 5.1 3.4 - - + -
237A LEU* 5.9 0.2 - - + -
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Residues in contact with THR 115 (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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90A ASP* 3.3 42.2 - - - +
92A ALA* 4.7 16.2 - - + +
93A THR 5.8 1.0 - - - +
94A ARG 5.0 2.0 - - - +
95A THR* 4.7 23.7 - - + +
111A ILE 3.7 8.0 + - - -
112A ALA* 3.8 9.1 + - - -
114A LEU* 1.4 66.3 - - - +
116A LEU* 1.3 63.0 + - - +
117A ASN* 3.4 3.0 - - - -
118A GLU* 4.6 5.2 - - - +
121A LEU* 4.3 10.6 - - + +
177A TRP* 3.5 26.5 - - + +
285A ARG* 5.1 0.3 + - - -
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Residues in contact with LEU 116 (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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93A THR 5.5 1.3 - - - +
95A THR* 5.8 1.1 - - - +
112A ALA 4.3 1.1 - - - +
113A SER* 3.4 33.0 - - - +
115A THR* 1.3 72.4 - - - +
117A ASN* 1.3 62.2 + - + +
118A GLU* 3.3 11.3 - - - +
265A SER* 3.8 26.0 - - - +
267A THR* 6.0 2.9 - - + -
285A ARG* 3.2 44.2 + - + +
287A PRO* 3.8 29.6 - - + -
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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