Contacts of the helix formed by residues 107 - 125 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLN* 4.0 8.1 - - - +
106B LEU* 1.3 85.5 - - - +
108B LYS* 1.3 57.9 + - - +
109B GLU* 3.6 7.6 + - - +
110B GLN* 2.9 34.8 + - - +
111B GLU* 2.7 23.2 + - - +
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Residues in contact with LYS 108 (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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107B SER* 1.3 74.4 - - - +
109B GLU* 1.3 62.4 + - + +
111B GLU* 3.7 18.9 - - + +
112B GLU* 3.7 9.4 + - - +
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Residues in contact with GLU 109 (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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107B SER* 3.1 7.6 + - - +
108B LYS* 1.3 76.1 - - + +
110B GLN* 1.3 64.4 + - + +
111B GLU 2.9 6.1 + - - -
112B GLU* 3.0 15.9 + - - +
113B LEU* 3.0 14.1 + - - +
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Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLN 3.9 3.6 - - - +
106B LEU* 3.1 22.0 - - + +
107B SER* 2.9 41.4 + - - +
109B GLU* 1.3 76.6 - - + +
111B GLU* 1.3 61.1 + - - +
113B LEU* 3.7 5.8 - - - +
114B ILE* 3.2 30.4 + - - +
290B LEU* 4.1 4.4 + - - +
291B THR* 3.4 43.1 + - + +
294B SER* 3.3 21.5 + - - -
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Residues in contact with GLU 111 (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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106B LEU* 2.6 38.9 - - - +
107B SER 2.7 24.2 + - - +
108B LYS* 3.7 16.8 - - + +
109B GLU 2.9 0.2 - - - -
110B GLN* 1.3 80.1 - - - +
112B GLU* 1.3 62.5 + - - +
114B ILE* 3.6 7.5 + - - +
115B ARG* 3.4 18.3 + - - +
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Residues in contact with GLU 112 (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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108B LYS 3.7 8.0 + - - +
109B GLU* 3.0 9.2 + - - +
111B GLU* 1.3 78.2 - - - +
113B LEU* 1.3 67.2 + - - +
115B ARG* 3.0 48.5 + - - +
116B THR* 3.1 27.6 + - - +
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Residues in contact with LEU 113 (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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109B GLU 3.0 11.5 + - - +
110B GLN* 3.7 10.5 - - - +
112B GLU* 1.3 78.2 - - - +
114B ILE* 1.3 62.2 + - - +
116B THR* 3.3 5.3 + - - -
117B LEU* 3.2 36.3 + - + +
181B VAL* 6.3 2.9 - - + -
261B LEU* 4.9 3.4 - - + -
287B GLU* 4.6 9.9 - - - +
288B MET* 3.9 35.9 - - + -
291B THR* 3.3 39.3 - - + +
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Residues in contact with ILE 114 (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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106B LEU* 4.8 14.6 - - + -
110B GLN 3.2 18.1 + - - +
111B GLU* 3.9 7.9 - - - +
112B GLU 3.2 0.2 - - - -
113B LEU* 1.3 75.7 - - - +
115B ARG* 1.3 61.3 + - - +
116B THR 3.4 0.3 + - - -
117B LEU* 3.5 9.4 + - + -
118B LEU* 3.2 42.5 + - + +
257B PRO* 4.1 17.7 - - + +
260B VAL* 6.2 0.2 - - + -
261B LEU* 4.7 19.7 - - + -
291B THR* 4.7 7.2 - - + -
295B TYR* 4.1 28.5 - - + -
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Residues in contact with ARG 115 (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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111B GLU 3.4 11.8 + - - +
112B GLU* 3.0 38.8 + - - +
114B ILE* 1.3 78.9 - - - +
116B THR* 1.3 57.2 + - - +
118B LEU* 4.6 5.0 - - - +
119B GLY* 3.5 18.0 + - - -
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Residues in contact with THR 116 (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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112B GLU* 3.1 25.0 + - - +
113B LEU* 3.3 5.5 + - - -
115B ARG* 1.3 75.0 - - - +
117B LEU* 1.3 66.7 + - - +
118B LEU 3.3 1.8 - - - -
119B GLY* 3.6 3.3 - - - +
120B ALA* 3.3 21.5 + - - +
178B ASP 4.3 15.1 - - - +
179B LEU* 4.6 4.6 - - + +
180B PRO* 4.4 20.0 - - + -
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Residues in contact with LEU 117 (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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113B LEU* 3.2 29.2 + - + +
114B ILE* 3.5 12.5 + - + +
116B THR* 1.3 78.1 - - - +
118B LEU* 1.3 58.8 + - + +
121B HIS* 2.9 28.1 + - - +
175B PHE* 3.5 24.1 - - + -
179B LEU* 5.3 8.5 - - + -
260B VAL* 3.2 30.4 - - + +
261B LEU* 3.3 37.2 - - + +
264B ALA* 4.0 21.8 - - + -
288B MET* 5.8 1.1 - - - -
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Residues in contact with LEU 118 (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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114B ILE* 3.2 35.3 + - + +
115B ARG* 4.6 4.5 - - - +
116B THR 3.3 0.2 - - - -
117B LEU* 1.3 78.8 - - + +
119B GLY* 1.3 68.6 + - - +
120B ALA 3.2 0.2 - - - -
121B HIS* 3.8 6.7 - - - +
122B THR* 2.8 33.7 + - - +
256B GLU* 3.8 26.2 - - + +
257B PRO* 4.7 9.9 - - + -
260B VAL* 3.5 30.5 - - + -
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Residues in contact with GLY 119 (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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115B ARG 3.5 13.6 + - - -
116B THR* 3.3 8.6 + - - -
117B LEU 3.3 0.8 - - - -
118B LEU* 1.3 81.6 - - - +
120B ALA* 1.3 56.0 + - - +
122B THR* 4.8 0.3 - - - -
123B ARG* 2.9 49.3 + - - +
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Residues in contact with ALA 120 (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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116B THR 3.3 11.2 + - - +
119B GLY* 1.3 73.6 - - - +
121B HIS* 1.3 62.6 + - - +
123B ARG* 3.9 1.8 - - - +
124B HIS* 3.0 30.9 + - - +
175B PHE* 3.5 24.1 - - + +
178B ASP* 3.1 49.8 - - + +
179B LEU* 4.3 1.3 - - + -
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Residues in contact with HIS 121 (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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117B LEU 2.9 22.2 + - - +
118B LEU* 3.1 6.5 + - - -
120B ALA* 1.3 74.7 - - - +
122B THR* 1.3 61.5 + - - +
123B ARG 3.1 1.8 - - - -
125B MET* 2.7 72.0 + - + +
126B GLY* 3.9 26.0 + - - -
175B PHE* 3.9 11.7 - - + -
205B VAL* 4.6 8.3 - - + +
256B GLU* 3.5 31.3 + - + -
260B VAL* 4.4 21.1 - - + +
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Residues in contact with THR 122 (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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118B LEU* 2.8 26.0 + - - +
119B GLY* 4.8 1.1 - - - -
121B HIS* 1.3 85.4 + - - +
123B ARG* 1.3 61.0 + - + +
125B MET 4.0 3.5 - - - +
127B THR* 4.0 27.5 + - + +
256B GLU* 4.0 10.6 + - - -
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Residues in contact with ARG 123 (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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119B GLY* 2.9 35.9 + - - +
120B ALA 4.0 0.4 - - - +
121B HIS 3.1 1.0 - - - -
122B THR* 1.3 81.1 - - + +
124B HIS* 1.3 78.7 + - + +
127B THR* 5.7 0.9 - - - -
171B GLN* 5.1 0.2 + - - -
178B ASP* 3.7 30.3 + - - -
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Residues in contact with HIS 124 (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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120B ALA 3.0 22.5 + - - +
121B HIS 3.3 1.8 + - - -
122B THR 3.4 0.2 - - - -
123B ARG* 1.3 93.7 + - + +
125B MET* 1.3 65.7 + - + +
127B THR* 5.3 1.5 + - - -
128B MET* 3.7 15.3 + - - +
131B GLN* 5.5 0.5 - - - +
171B GLN* 3.1 39.4 + - - +
174B LYS* 3.2 56.7 + - + +
175B PHE* 3.9 3.2 - - - +
178B ASP* 2.9 29.1 + - - -
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Residues in contact with MET 125 (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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121B HIS* 2.7 47.6 + - + +
122B THR* 4.0 5.4 - - - +
124B HIS* 1.3 79.8 - - - +
126B GLY* 1.3 59.5 + - - +
127B THR* 2.8 17.4 + - - -
128B MET* 4.0 14.4 - - + -
171B GLN* 4.2 10.8 - - + +
172B VAL* 4.1 19.5 - - - -
175B PHE* 3.9 52.5 - - + -
201B ILE* 4.6 5.4 - - + -
205B VAL* 4.0 28.7 - - + -
263B ALA* 5.4 5.4 - - + -
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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