Contacts of the helix formed by residues 114 - 129 (chain D) in PDB entry 1Y67
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D ILE* 3.8 5.9 - - - +
109D ASN* 3.4 14.4 + - - +
112D PHE* 3.3 3.7 + - - +
113D GLY* 1.3 79.2 - - - +
115D PHE* 1.3 57.6 + - - +
116D ASP* 3.7 7.9 + - - +
117D ALA* 3.1 23.4 + - - +
118D PHE* 3.0 28.1 + - - +
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Residues in contact with PHE 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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98D ASN 3.6 22.7 - - - -
99D GLN* 3.7 22.2 - - + +
100D PRO* 3.4 29.4 - - + -
105D LEU* 4.3 15.7 - - + -
108D ILE* 3.9 10.3 - - + -
109D ASN* 3.7 6.1 + - - -
114D SER* 1.3 70.5 - - - +
116D ASP* 1.3 68.5 + - - +
118D PHE* 3.4 17.1 + + - +
119D LYS* 3.0 56.2 + - + +
195D TRP* 4.9 1.8 - + + -
200D TRP* 3.5 31.4 - + - -
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Residues in contact with ASP 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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114D SER* 3.3 8.1 + - - +
115D PHE* 1.3 83.1 - - - +
117D ALA* 1.3 60.8 + - - +
119D LYS* 3.2 26.6 + - - +
120D GLN* 3.1 21.8 + - - +
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Residues in contact with ALA 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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112D PHE* 3.3 26.2 - - - +
113D GLY 5.0 0.2 - - - -
114D SER* 3.1 18.4 + - - +
116D ASP* 1.3 73.3 - - - +
118D PHE* 1.3 65.8 + - - +
120D GLN* 3.4 11.4 + - - +
121D LYS* 3.0 23.6 + - - +
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Residues in contact with PHE 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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108D ILE* 3.7 11.7 - - + -
112D PHE* 3.7 42.7 - + + +
114D SER 3.0 13.6 + - - +
115D PHE* 3.5 24.0 - + - +
116D ASP 3.3 0.2 - - - -
117D ALA* 1.3 77.4 - - - +
119D LYS* 1.3 59.4 - - - +
121D LYS* 3.2 2.0 + - - +
122D PHE* 2.8 46.6 + + + +
137D LEU* 3.7 35.4 - - + -
146D VAL* 3.9 13.2 - - + -
170D LEU* 4.2 7.2 - - + -
195D TRP* 3.7 22.4 - + - -
200D TRP* 3.8 18.4 - + - -
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Residues in contact with LYS 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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98D ASN 5.2 2.2 + - - -
115D PHE* 3.0 52.3 + - + +
116D ASP* 3.2 28.7 + - - +
118D PHE* 1.3 76.8 - - + +
120D GLN* 1.3 56.2 + - - +
122D PHE* 3.7 1.2 - - - +
123D GLU* 2.9 38.0 + - - +
195D TRP* 3.6 56.5 - - + +
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Residues in contact with GLN 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 ASP 3.1 11.9 + - - +
117D ALA* 3.7 11.8 - - - +
118D PHE 3.3 0.2 - - - -
119D LYS* 1.3 77.1 - - - +
121D LYS* 1.3 57.0 + - - +
123D GLU* 3.8 5.6 - - - +
124D ASP* 2.9 31.8 + - + +
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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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112D PHE* 4.0 24.7 - - + -
117D ALA 3.0 17.1 + - - +
118D PHE* 3.7 6.7 - - - +
120D GLN* 1.3 76.5 - - - +
122D PHE* 1.3 62.0 + - - +
124D ASP* 3.3 6.4 + - + +
125D ALA* 3.1 22.7 + - + +
145D ASP* 3.6 20.5 + - - -
146D VAL* 4.1 23.1 - - + -
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Residues in contact with PHE 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 PHE* 2.8 37.4 + + + +
119D LYS 3.7 3.1 - - - +
121D LYS* 1.3 76.5 - - - +
123D GLU* 1.3 65.2 + - + +
125D ALA* 3.2 5.0 + - - +
126D ALA* 3.0 22.2 + - + +
135D ALA* 3.7 13.7 - - + +
136D TRP* 3.8 32.5 - - - -
137D LEU 3.8 3.1 - - - -
146D VAL* 3.8 10.9 - - + +
170D LEU* 4.3 16.6 - - + -
171D GLY 4.3 3.4 - - - -
172D VAL* 3.5 43.3 - - + -
191D LEU* 5.5 2.2 - - + -
194D PHE* 4.3 8.5 - + - -
195D TRP* 3.3 31.4 - + + -
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Residues in contact with GLU 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 LYS* 2.9 22.9 + - - +
120D GLN* 3.8 5.4 - - - +
122D PHE* 1.3 78.2 - - + +
124D ASP* 1.3 51.9 + - - +
126D ALA* 3.2 8.0 + - - +
127D LYS* 2.7 56.9 + - - +
188D PRO* 4.5 4.9 - - - +
191D LEU* 3.8 29.6 - - + +
192D ALA* 3.8 9.8 + - - +
195D TRP* 2.8 37.5 + - + +
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Residues in contact with ASP 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 GLN* 2.9 21.4 + - + +
121D LYS* 3.7 7.6 - - + +
122D PHE 3.2 0.2 - - - -
123D GLU* 1.3 73.5 - - - +
125D ALA* 1.3 59.3 + - - +
127D LYS* 3.8 14.9 + - - +
128D THR* 2.9 49.6 + - - +
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Residues in contact with ALA 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 LYS 3.1 6.9 + - - +
122D PHE 3.5 3.4 - - - +
124D ASP* 1.3 77.2 + - - +
126D ALA* 1.3 60.6 + - - +
128D THR* 3.5 7.4 + - - -
129D ARG* 3.3 23.0 + - - +
135D ALA* 4.2 9.9 - - + -
146D VAL* 3.5 32.8 - - + +
147D VAL* 4.5 11.4 - - - +
148D SER* 3.9 8.8 + - - -
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Residues in contact with ALA 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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122D PHE* 3.0 13.0 + - + +
123D GLU* 3.5 7.9 - - - +
125D ALA* 1.3 78.1 - - - +
127D LYS* 1.3 57.8 + - - +
129D ARG* 3.6 8.7 + - - +
135D ALA* 3.7 20.4 - - + +
172D VAL* 4.2 2.7 - - + -
174D VAL* 4.0 10.1 - - + +
187D ARG* 2.9 25.8 + - - -
191D LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 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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120D GLN 5.7 0.2 - - - -
123D GLU* 2.7 43.2 + - - +
124D ASP* 3.9 12.8 + - - +
126D ALA* 1.3 74.1 - - - +
128D THR* 1.3 64.0 + - + +
129D ARG 3.5 1.6 + - - +
187D ARG* 3.9 15.9 + - - +
188D PRO* 4.2 31.4 - - + +
191D LEU* 3.6 16.6 - - + -
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Residues in contact with THR 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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124D ASP* 2.9 39.8 + - - +
125D ALA* 3.5 10.6 + - - -
126D ALA 3.4 0.2 - - - -
127D LYS* 1.3 78.1 - - + +
129D ARG* 1.3 58.8 + - - +
130D PHE* 3.0 13.0 + - - +
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Residues in contact with ARG 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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125D ALA 3.3 15.9 + - - +
126D ALA* 3.7 9.0 - - - +
127D LYS 3.3 2.9 - - - +
128D THR* 1.3 73.5 - - - +
130D PHE* 1.3 71.3 + - - +
131D GLY 3.6 0.4 - - - +
132D SER 3.9 12.3 - - - +
133D GLY* 4.1 7.2 - - - +
134D TRP 4.3 2.0 - - - +
148D SER* 2.9 47.2 + - - +
149D THR* 3.2 24.5 + - - +
150D ALA* 3.5 22.8 - - - +
174D VAL* 3.9 20.4 - - + -
187D ARG* 2.8 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