Contacts of the helix formed by residues 119 - 134 (chain D) in PDB entry 1Y1V
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 ARG 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D THR* 1.3 71.7 - - + +
120D GLU* 1.3 73.5 + - + +
121D LYS 3.0 0.7 - - - -
122D GLU* 2.9 26.3 + - - +
123D LEU* 3.5 12.7 + - + +
149D THR* 5.2 9.2 - - - +
150D ASN* 4.9 14.1 - - - +
221D TYR* 4.0 48.9 - - + +
142G ARG* 6.1 2.2 - - - +
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Residues in contact with GLU 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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118D THR 2.8 3.1 + - - +
119D ARG* 1.3 85.9 - - + +
121D LYS* 1.3 62.3 + - + +
122D GLU 3.6 0.2 + - - -
123D LEU* 3.6 34.8 + - + +
124D GLU* 4.0 6.9 + - - +
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Residues in contact with LYS 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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118D THR* 2.9 44.3 + - + +
120D GLU* 1.3 78.7 - - + +
122D GLU* 1.3 60.1 + - - +
124D GLU* 3.8 4.9 + - - +
125D SER* 3.2 22.3 + - - -
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Residues in contact with GLU 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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56D ARG* 3.0 36.5 + - - -
60D LYS* 3.9 17.5 + - - +
118D THR 4.4 10.3 + - - +
119D ARG* 2.9 14.0 + - - +
121D LYS* 1.3 77.0 - - - +
123D LEU* 1.3 67.8 + - - +
124D GLU 3.1 0.4 - - - -
125D SER* 3.0 11.5 + - - +
126D ILE* 2.9 37.2 + - + +
149D THR* 2.6 31.2 + - + +
155D ARG* 4.6 15.9 + - - +
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Residues in contact with LEU 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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119D ARG* 4.0 10.1 - - + +
120D GLU* 3.7 31.6 - - + +
122D GLU* 1.3 78.4 - - - +
124D GLU* 1.3 57.2 + - + +
126D ILE* 3.8 4.4 - - - +
127D ASP* 3.1 35.7 + - - +
146D GLN* 4.5 23.8 - - + +
149D THR* 3.3 29.8 - - + -
150D ASN* 3.7 20.9 - - - +
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Residues in contact with GLU 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 GLU 4.0 6.1 + - - +
121D LYS* 3.8 6.8 + - - +
122D GLU 3.1 0.2 - - - -
123D LEU* 1.3 76.8 - - + +
125D SER* 1.3 65.5 + - - +
126D ILE 2.8 6.2 + - - -
127D ASP* 3.0 19.1 + - + +
128D VAL* 3.3 17.4 + - + +
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Residues in contact with SER 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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60D LYS* 5.8 0.3 + - - -
67D ARG* 5.7 0.7 + - - -
121D LYS 3.2 9.2 + - - -
122D GLU* 3.0 34.7 + - - +
124D GLU* 1.3 77.3 - - - +
126D ILE* 1.3 60.4 + - - +
128D VAL* 3.9 7.3 - - - +
129D LEU* 3.7 15.1 + - - +
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Residues in contact with ILE 126 (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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56D ARG* 5.3 2.2 - - + -
60D LYS* 4.8 15.5 - - + -
122D GLU* 2.9 32.6 + - + +
123D LEU* 3.8 4.5 - - - +
124D GLU 2.8 0.8 + - - -
125D SER* 1.3 77.8 - - - +
127D ASP* 1.3 63.0 + - - +
128D VAL 2.9 2.0 - - - -
129D LEU* 2.7 37.0 + - + +
130D LEU* 2.9 22.6 + - + +
145D MET* 4.2 41.5 - - + -
149D THR* 3.6 27.4 - - + +
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Residues in contact with ASP 127 (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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123D LEU* 3.1 20.4 + - - +
124D GLU* 3.0 11.2 + - + +
126D ILE* 1.3 83.0 - - - +
128D VAL* 1.3 51.5 + - + +
130D LEU* 3.4 13.1 + - - +
131D GLU* 2.8 48.2 + - + +
142D LYS* 5.6 5.4 - - - +
146D GLN* 5.6 8.9 + - - +
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Residues in contact with VAL 128 (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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67D ARG* 3.9 11.7 - - - +
124D GLU* 3.3 14.3 + - + +
125D SER* 3.9 10.1 - - - +
126D ILE 2.7 4.0 + - - -
127D ASP* 1.3 70.8 - - + +
129D LEU* 1.3 68.7 + - - +
130D LEU 3.0 0.9 - - - -
131D GLU* 2.9 17.8 + - + +
132D GLN* 2.8 43.3 + - + +
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Residues in contact with LEU 129 (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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60D LYS* 4.5 11.2 - - + +
63D LEU* 3.5 49.1 - - + +
64D VAL* 4.0 24.7 - - + +
67D ARG* 4.0 26.9 - - + +
125D SER 3.7 10.1 + - - +
126D ILE* 2.7 25.2 + - + +
128D VAL* 1.3 75.3 - - - +
130D LEU* 1.3 59.0 + - + +
132D GLN* 3.0 7.5 - - - +
133D THR* 3.0 34.8 + - + +
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Residues in contact with LEU 130 (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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63D LEU* 3.4 22.2 - - + -
126D ILE* 2.9 24.1 + - + +
127D ASP* 3.5 14.8 - - - +
129D LEU* 1.3 73.9 - - + +
131D GLU* 1.3 55.6 + - + +
132D GLN 2.5 16.4 + - - -
134D THR* 2.9 51.6 + - + +
141D LEU* 4.2 13.9 - - + -
142D LYS* 4.0 42.4 - - + +
145D MET* 4.2 17.7 - - + -
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Residues in contact with GLU 131 (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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127D ASP* 2.8 37.4 + - + +
128D VAL* 2.9 20.3 + - - +
130D LEU* 1.3 69.1 - - + +
132D GLN* 1.3 59.5 + - + +
134D THR 5.5 1.1 - - - -
142D LYS* 6.0 6.5 - - - +
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Residues in contact with GLN 132 (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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67D ARG* 2.9 43.8 + - - +
70D PHE* 4.4 11.8 - - - -
71D LYS* 4.1 15.6 + - - +
128D VAL* 2.8 28.2 + - + +
129D LEU* 3.0 15.0 - - - +
130D LEU 2.5 11.3 + - - -
131D GLU* 1.3 79.8 + - + +
133D THR* 1.3 64.9 + - + +
134D THR 3.8 1.9 - - - +
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Residues in contact with THR 133 (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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63D LEU* 3.0 39.8 + - - +
66D ARG* 3.7 35.0 + - + -
67D ARG* 3.6 40.4 - - + +
70D PHE* 4.5 20.3 - - + -
129D LEU* 3.0 10.2 + - + +
132D GLN* 1.3 80.8 - - + +
134D THR* 1.3 64.7 + - - +
135D GLY 4.2 0.2 + - - -
31G LEU* 5.9 0.2 - - - +
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Residues in contact with THR 134 (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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63D LEU* 3.9 5.7 - - - +
66D ARG* 5.4 0.7 - - - +
130D LEU* 2.9 50.8 + - + +
131D GLU 5.5 0.7 - - - -
132D GLN 5.0 1.6 - - - +
133D THR* 1.3 82.3 + - - +
135D GLY* 1.3 74.6 + - - +
136D GLY* 3.2 10.5 + - - +
138D ASN* 3.5 35.0 - - + +
141D LEU* 4.2 8.8 - - + +
142D LYS* 6.1 4.5 - - + -
35G GLU* 5.3 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