Contacts of the helix formed by residues 107 - 125 (chain D) in PDB entry 1XV9
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 SER 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D GLN* 4.9 7.8 - - - +
106D LEU* 1.3 83.5 - - - +
108D LYS* 1.3 59.6 + - - +
109D GLU* 3.0 25.1 + - - +
110D GLN* 3.4 21.3 + - - +
111D GLU* 2.8 16.0 + - - +
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Residues in contact with LYS 108 (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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107D SER* 1.3 73.2 - - - +
109D GLU* 1.3 58.0 + - + +
111D GLU* 4.0 15.3 - - + -
112D GLU* 3.4 28.8 + - + +
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Residues in contact with GLU 109 (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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107D SER* 3.0 13.1 + - - +
108D LYS* 1.3 77.3 - - + +
110D GLN* 1.3 63.4 + - + +
111D GLU 3.1 1.6 - - - -
112D GLU* 3.4 5.2 + - - +
113D LEU* 3.1 25.5 + - - +
287D GLU* 5.1 7.4 - - - +
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Residues in contact with GLN 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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105D GLN 3.6 2.9 - - - +
106D LEU* 3.1 35.3 - - + +
107D SER* 3.4 18.9 + - - +
109D GLU* 1.3 77.8 - - + +
111D GLU* 1.3 64.5 + - - +
113D LEU* 3.4 4.1 - - - +
114D ILE* 3.3 30.5 + - - +
290D LEU* 4.4 7.3 - - - +
291D THR* 3.5 38.6 + - + +
294D SER* 3.6 19.8 + - - -
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Residues in contact with GLU 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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106D LEU* 3.0 43.9 - - - +
107D SER 2.8 25.7 + - - +
108D LYS* 4.0 18.8 - - + +
110D GLN* 1.3 76.9 - - - +
112D GLU* 1.3 64.4 + - - +
113D LEU 3.1 0.2 - - - -
114D ILE* 3.6 5.2 + - - +
115D ARG* 3.1 25.4 + - - +
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Residues in contact with GLU 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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108D LYS* 3.4 22.1 + - + +
109D GLU* 3.8 5.2 - - - +
111D GLU* 1.3 79.4 - - - +
113D LEU* 1.3 54.2 + - - +
115D ARG* 4.0 13.4 - - - +
116D THR* 2.6 61.5 + - - +
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Residues in contact with LEU 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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109D GLU 3.1 12.7 + - - +
110D GLN* 3.4 9.6 - - - +
111D GLU 3.1 0.2 - - - -
112D GLU* 1.3 73.5 - - - +
114D ILE* 1.3 68.5 + - - +
116D THR* 2.9 8.5 + - - -
117D LEU* 2.9 38.2 + - + +
261D LEU* 4.6 6.5 - - + -
287D GLU* 4.0 15.0 - - + +
288D MET* 3.8 40.8 - - + -
291D THR* 3.0 40.2 - - + +
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Residues in contact with ILE 114 (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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106D LEU* 4.3 20.4 - - + -
110D GLN 3.3 16.9 + - - +
111D GLU* 4.2 6.3 - - - +
113D LEU* 1.3 74.7 - - - +
115D ARG* 1.3 55.4 + - - +
117D LEU* 4.0 7.2 - - - -
118D LEU* 3.0 37.8 + - + +
257D PRO* 3.6 26.5 - - + -
261D LEU* 3.8 27.1 - - + -
291D THR* 4.2 4.3 - - + +
295D TYR* 3.6 30.1 - - + -
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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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111D GLU 3.1 20.1 + - - +
112D GLU* 3.6 18.6 - - - +
113D LEU 3.0 0.6 - - - -
114D ILE* 1.3 74.3 - - - +
116D THR* 1.3 56.0 + - - +
118D LEU* 4.3 2.1 - - - +
119D GLY* 2.7 38.0 + - - -
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Residues in contact with THR 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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112D GLU* 2.6 39.0 + - - +
113D LEU* 3.5 5.8 - - - -
115D ARG* 1.3 78.0 - - - +
117D LEU* 1.3 56.6 + - + +
119D GLY* 3.1 1.8 + - - -
120D ALA* 2.8 29.6 + - - +
123D ARG* 5.2 0.2 + - - -
178D ASP 5.0 1.6 - - - +
179D LEU* 3.7 21.5 - - + -
180D PRO* 4.5 15.7 - - + -
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Residues in contact with LEU 117 (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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113D LEU* 2.9 30.7 + - + +
114D ILE* 4.1 4.0 - - - +
116D THR* 1.3 76.7 - - - +
118D LEU* 1.3 51.7 + - - +
119D GLY 3.1 0.3 + - - -
120D ALA 3.1 1.4 + - - -
121D HIS* 2.6 37.1 + - - +
175D PHE* 3.5 13.0 - - + -
179D LEU* 3.9 31.4 - - + -
260D VAL* 3.1 20.2 - - + +
261D LEU* 3.1 33.0 - - + -
264D ALA* 3.8 23.8 - - + -
268D PHE* 6.2 3.1 - - + -
288D MET* 4.8 0.4 - - - -
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Residues in contact with LEU 118 (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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114D ILE* 3.0 27.3 + - + +
115D ARG* 4.3 2.0 - - - +
117D LEU* 1.3 75.5 - - + +
119D GLY* 1.3 66.3 + - - +
121D HIS* 4.0 6.1 - - - -
122D THR* 2.9 28.1 + - - -
256D GLU* 3.5 24.2 - - - +
257D PRO* 3.3 41.5 - - + -
260D VAL* 3.2 34.5 - - + -
261D LEU* 5.7 0.4 - - + -
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Residues in contact with GLY 119 (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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115D ARG* 2.7 27.1 + - - -
116D THR* 3.4 2.5 - - - -
117D LEU 3.0 0.4 - - - -
118D LEU* 1.3 81.4 - - - +
120D ALA* 1.3 58.4 + - - +
122D THR* 4.2 1.6 - - - -
123D ARG* 2.9 43.5 + - - +
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Residues in contact with ALA 120 (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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116D THR 2.8 16.0 + - - +
117D LEU 3.9 1.1 - - - +
119D GLY* 1.3 69.4 - - - -
121D HIS* 1.3 63.4 + - - +
123D ARG* 3.7 4.7 - - - +
124D HIS* 3.1 27.2 + - - +
175D PHE* 3.3 23.7 - - + +
178D ASP* 3.3 44.2 - - + +
179D LEU* 4.0 5.4 - - + -
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Residues in contact with HIS 121 (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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117D LEU 2.6 21.9 + - - +
118D LEU* 4.4 1.0 - - - -
120D ALA* 1.3 70.1 - - - +
122D THR* 1.3 60.8 + - + +
123D ARG 3.1 1.3 - - - -
125D MET* 2.5 63.8 + - + +
126D GLY* 4.0 17.1 - - - -
175D PHE* 3.3 18.8 - - + -
205D VAL* 4.9 6.5 - - + +
208D THR* 6.0 3.6 - - + +
256D GLU* 3.7 34.9 + - + -
259D TYR* 6.0 3.2 - - + +
260D VAL* 3.2 29.0 - - + +
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Residues in contact with THR 122 (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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118D LEU* 2.9 19.3 + - - +
119D GLY 4.3 1.8 - - - -
121D HIS* 1.3 82.0 + - + +
123D ARG* 1.3 62.5 + - - +
124D HIS 3.6 0.3 + - - -
125D MET 3.7 3.8 - - - +
126D GLY* 5.8 0.2 - - - -
127D THR* 3.3 30.0 - - + +
256D GLU* 3.2 24.3 + - - +
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Residues in contact with ARG 123 (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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116D THR 5.2 0.4 + - - -
119D GLY* 2.9 49.0 + - - +
120D ALA* 3.4 8.8 - - - +
122D THR* 1.3 82.7 - - - +
124D HIS* 1.3 71.7 + - + +
127D THR* 4.2 4.5 + - - -
178D ASP* 3.4 25.6 + - - -
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Residues in contact with HIS 124 (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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120D ALA 3.1 16.1 + - - +
123D ARG* 1.3 91.5 - - + +
125D MET* 1.3 68.7 + - + +
127D THR* 3.4 12.7 + - - -
128D MET* 3.9 8.0 - - - +
131D GLN* 5.5 0.9 - - - +
171D GLN* 3.2 26.3 + - - +
174D LYS* 3.2 38.5 + - + +
175D PHE* 3.8 17.1 - - - +
178D ASP* 3.6 35.2 - - + +
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Residues in contact with MET 125 (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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121D HIS* 2.5 41.5 + - + +
122D THR* 3.7 8.8 - - - +
124D HIS* 1.3 75.9 - - - +
126D GLY* 1.3 59.6 + - - +
127D THR* 2.8 12.1 + - - +
128D MET* 3.7 11.7 - - + +
171D GLN* 3.6 34.5 - - + +
172D VAL* 3.6 27.4 - - - -
175D PHE* 3.8 27.4 - - + -
201D ILE* 4.2 6.7 - - + -
205D VAL* 3.2 38.8 - - + -
263D ALA* 5.8 1.8 - - + -
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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