Contacts of the helix formed by residues 115 - 130 (chain A) in PDB entry 1V0D
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLN* 1.3 79.4 - - - +
116A PRO* 1.3 70.0 - - + +
117A LEU* 3.4 4.3 - - + +
118A ARG* 4.4 13.4 - - + +
119A GLN* 2.9 27.7 + - - +
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Residues in contact with PRO 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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114A GLN 3.7 1.9 - - - +
115A ALA* 1.3 87.5 - - + +
117A LEU* 1.3 60.3 + - + +
119A GLN* 3.5 11.4 - - + +
120A LYS* 3.0 28.5 + - - +
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Residues in contact with LEU 117 (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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115A ALA* 3.4 3.0 - - + +
116A PRO* 1.3 80.8 - - + +
118A ARG* 1.3 67.5 + - - +
120A LYS* 3.0 20.4 + - + +
121A LEU* 3.1 15.5 + - - +
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Residues in contact with ARG 118 (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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114A GLN* 4.5 18.4 - - + +
115A ALA* 3.5 18.1 + - + +
117A LEU* 1.3 79.5 - - - +
119A GLN* 1.3 62.0 + - - +
121A LEU* 3.6 7.2 + - - +
122A LEU* 3.0 27.3 + - - +
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Residues in contact with GLN 119 (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 LEU* 3.8 16.6 - - + +
113A GLU* 5.1 5.5 - - - +
114A GLN* 4.0 25.3 + - + +
115A ALA 2.9 17.6 + - - +
116A PRO* 3.5 9.7 + - - +
118A ARG* 1.3 77.7 - - - +
120A LYS* 1.3 53.0 + - - +
122A LEU* 3.4 5.9 + - - +
123A ALA* 2.8 35.4 + - + +
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Residues in contact with LYS 120 (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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116A PRO 3.0 15.0 + - - +
117A LEU* 3.1 18.2 - - + +
119A GLN* 1.3 73.5 - - - +
121A LEU* 1.3 67.8 + - - +
123A ALA* 2.8 18.7 + - + +
124A ASP* 2.8 53.0 + - - +
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Residues in contact with LEU 121 (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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117A LEU 3.1 9.9 + - - +
118A ARG* 3.9 7.0 - - - +
120A LYS* 1.3 78.3 - - - +
122A LEU* 1.3 52.4 + - - +
124A ASP* 3.3 10.5 + - + +
125A LEU* 2.8 60.5 + - + +
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Residues in contact with LEU 122 (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 PHE* 6.2 2.2 - - + -
106A ALA* 3.8 21.0 - - + +
109A GLN* 3.3 45.3 - - + +
110A LEU* 3.6 16.5 - - + +
114A GLN* 3.2 27.4 - - - +
118A ARG 3.0 17.6 + - - +
119A GLN 3.5 4.5 - - - +
121A LEU* 1.3 76.4 - - - +
123A ALA* 1.3 64.8 + - - +
125A LEU* 3.4 14.8 + - + +
126A LEU* 3.0 23.9 + - - +
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Residues in contact with ALA 123 (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 LEU* 3.9 18.5 - - + +
119A GLN* 2.8 17.3 + - + +
120A LYS* 2.8 15.1 + - + +
122A LEU* 1.3 72.1 - - - +
124A ASP* 1.3 65.3 + - - +
126A LEU* 3.4 4.3 + - - +
127A HIS* 3.0 21.3 + - - +
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Residues in contact with ASP 124 (chain A).
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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120A LYS* 2.8 55.6 + - - +
121A LEU* 3.5 11.2 + - + +
123A ALA* 1.3 79.1 - - - +
125A LEU* 1.3 53.8 + - + +
127A HIS* 2.9 14.7 + - - +
128A HIS* 2.7 34.9 + - - +
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Residues in contact with LEU 125 (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 PHE* 3.7 61.0 - - + +
106A ALA* 5.7 3.4 - - + -
121A LEU* 2.8 46.3 + - + +
122A LEU* 3.7 16.4 - - + +
124A ASP* 1.3 72.2 - - + +
126A LEU* 1.3 65.1 + - - +
128A HIS* 3.1 13.4 + - + +
129A VAL* 2.9 30.3 + - + +
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Residues in contact with LEU 126 (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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103A ILE* 4.0 16.4 - - + +
106A ALA* 4.2 16.4 - - + +
107A ARG* 3.4 42.8 - - + +
110A LEU* 3.5 23.3 - - + -
122A LEU 3.0 12.0 + - - +
123A ALA 3.6 9.2 - - - +
125A LEU* 1.3 75.3 - - - +
127A HIS* 1.3 54.4 + - - +
129A VAL* 4.8 3.8 - - + -
130A SER* 2.7 65.2 + - - +
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Residues in contact with HIS 127 (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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123A ALA 3.0 13.2 + - - +
124A ASP* 2.9 17.0 + - - +
126A LEU* 1.3 79.2 - - - +
128A HIS* 1.3 67.2 + - - +
129A VAL 3.1 0.9 + - - -
130A SER* 3.3 9.9 + - - +
131A GLN* 4.5 1.6 - - - +
249A ASN* 3.0 52.0 + - - +
251A GLU* 4.1 30.3 + - + +
252A SER* 4.3 7.1 + - - -
255A LEU* 4.5 15.7 - - + -
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Residues in contact with HIS 128 (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 PHE 3.9 15.9 + - - -
96A ASN* 3.6 37.1 + - - +
124A ASP 2.7 15.5 + - - +
125A LEU* 3.1 19.7 + - + +
127A HIS* 1.3 77.9 + - - +
129A VAL* 1.3 62.0 + - + +
131A GLN* 3.9 15.9 - - - +
226A TRP* 6.3 1.2 - - - -
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Residues in contact with VAL 129 (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 PHE* 3.3 37.9 - - + +
96A ASN 4.9 0.9 - - - +
98A PRO* 3.3 48.6 - - + +
102A VAL* 5.9 7.0 - - + -
103A ILE* 3.6 24.9 - - + +
125A LEU* 2.9 20.7 + - + +
126A LEU* 4.0 4.3 - - + +
128A HIS* 1.3 78.4 - - + +
130A SER* 1.3 51.8 + - - +
131A GLN* 2.4 23.7 + - - +
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Residues in contact with SER 130 (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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103A ILE* 4.2 9.5 - - - +
107A ARG* 3.9 15.7 + - - -
126A LEU* 2.7 43.3 + - - +
127A HIS* 3.8 5.2 - - - -
129A VAL* 1.3 68.1 - - - +
131A GLN* 1.3 57.3 + - - +
248A GLY 4.3 0.2 - - - +
249A ASN* 3.3 20.3 + - - +
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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