Contacts of the helix formed by residues 114 - 129 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.7 5.8 - - - +
109A ASN* 3.4 14.8 - - - +
112A PHE* 3.4 2.6 + - - +
113A GLY* 1.3 80.4 - - - +
115A PHE* 1.3 65.8 + - - +
116A ASP* 3.6 8.4 + - - +
117A ALA* 3.0 23.7 + - - +
118A PHE* 2.9 23.9 + - - +
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Residues in contact with PHE 115 (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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98A ASN 3.8 9.6 - - - -
99A GLN* 3.5 35.9 - - + +
100A PRO* 3.4 30.5 - - + -
105A LEU* 4.1 15.5 - - + +
108A ILE* 3.8 11.2 - - + +
109A ASN* 3.7 6.9 + - - -
114A SER* 1.3 73.1 - - - +
116A ASP* 1.3 63.0 + - - +
118A PHE* 3.2 22.9 + + - +
119A LYS* 2.9 63.4 + - + +
195A TRP* 4.5 2.9 - + + -
200A TRP* 3.5 28.5 - + - -
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Residues in contact with ASP 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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99A GLN* 5.5 0.9 - - - +
114A SER* 3.2 7.1 + - - +
115A PHE* 1.3 82.6 - - - +
117A ALA* 1.3 62.0 + - - +
119A LYS* 3.3 28.6 + - - +
120A GLN* 3.1 25.3 + - - +
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Residues in contact with ALA 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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112A PHE* 3.3 25.4 - - - +
113A GLY* 4.8 0.7 - - - -
114A SER* 3.0 20.8 + - - +
116A ASP* 1.3 72.7 - - - +
118A PHE* 1.3 66.5 + - - +
120A GLN* 3.3 10.0 + - - +
121A LYS* 3.0 22.9 + - - +
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Residues in contact with PHE 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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108A ILE* 3.6 19.5 - - + -
112A PHE* 3.8 31.1 - + + +
114A SER 2.9 14.0 + - - +
115A PHE* 3.4 24.9 - + - +
117A ALA* 1.3 72.4 - - - +
119A LYS* 1.3 63.5 + - - +
121A LYS* 3.1 3.4 + - - +
122A PHE* 2.8 42.9 + + + +
137A LEU* 3.8 28.5 - - + -
146A VAL* 3.8 24.2 - - + -
170A LEU* 4.3 5.2 - - + -
195A TRP* 3.6 34.5 - + - -
200A TRP* 3.8 14.1 - + - -
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Residues in contact with LYS 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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97A ALA* 5.9 5.1 - - - +
98A ASN 5.3 2.0 + - - -
115A PHE* 2.9 47.8 + - + +
116A ASP* 3.6 31.3 + - - +
117A ALA 3.3 0.2 - - - -
118A PHE* 1.3 77.1 - - + +
120A GLN* 1.3 58.0 + - + +
122A PHE* 3.7 0.9 - - - +
123A GLU* 2.8 39.4 + - - +
195A TRP* 3.6 55.5 - - + +
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Residues in contact with GLN 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 ASP 3.1 16.1 + - - +
117A ALA* 3.4 12.1 - - - +
118A PHE 3.2 0.2 - - - -
119A LYS* 1.3 77.8 - - - +
121A LYS* 1.3 57.1 + - - +
123A GLU* 3.8 16.2 + - - +
124A ASP* 2.9 49.6 + - - +
127A LYS* 5.7 4.6 + - - +
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Residues in contact with LYS 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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112A PHE* 4.4 20.6 - - + -
117A ALA 3.0 13.5 + - - +
118A PHE* 3.5 10.3 - - - +
120A GLN* 1.3 72.7 - - - +
122A PHE* 1.3 60.9 + - - +
124A ASP* 3.4 7.9 + - + +
125A ALA* 3.1 27.9 + - - +
145A ASP* 4.6 10.6 + - - -
146A VAL* 3.8 30.7 + - + +
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Residues in contact with PHE 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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118A PHE* 2.8 35.5 + + + +
119A LYS 3.7 2.9 - - - +
121A LYS* 1.3 74.8 - - - +
123A GLU* 1.3 67.7 + - + +
125A ALA* 3.3 2.9 + - - +
126A ALA* 3.0 20.9 + - + +
135A ALA* 3.7 11.2 - - + +
136A TRP* 3.7 35.4 - - - -
137A LEU 3.8 3.8 - - - -
146A VAL* 3.8 11.4 - - + -
170A LEU* 4.4 16.8 - - + -
171A GLY 4.4 1.6 - - - -
172A VAL* 3.4 42.2 - - + -
191A LEU* 5.4 2.9 - - + -
194A PHE* 4.3 8.5 - + - -
195A TRP* 3.4 31.6 - + + -
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Residues in contact with GLU 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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119A LYS* 2.8 27.3 + - - +
120A GLN* 3.9 17.9 + - - +
122A PHE* 1.3 73.2 - - + +
124A ASP* 1.3 59.5 + - - +
126A ALA* 3.4 2.6 + - - +
127A LYS* 2.8 50.0 + - - +
188A PRO* 4.7 5.0 - - - +
191A LEU* 4.1 28.1 - - + +
192A ALA* 4.2 10.8 + - - +
195A TRP* 2.7 37.5 + - + +
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Residues in contact with ASP 124 (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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120A GLN* 2.9 39.8 + - - +
121A LYS* 3.7 8.2 - - + +
122A PHE 3.2 0.2 - - - -
123A GLU* 1.3 74.7 - - - +
125A ALA* 1.3 53.6 + - - +
127A LYS* 3.3 23.3 + - - +
128A THR* 2.7 46.1 + - + +
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Residues in contact with ALA 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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121A LYS 3.1 7.3 + - - +
122A PHE 3.7 2.5 - - - +
124A ASP* 1.3 76.1 - - - +
126A ALA* 1.3 61.1 + - - +
128A THR* 3.4 7.1 + - - -
129A ARG* 3.3 22.7 + - - +
135A ALA* 4.3 4.0 - - + -
146A VAL* 3.5 33.2 - - + +
147A VAL 4.4 15.9 - - - +
148A SER* 3.9 9.4 + - - -
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Residues in contact with ALA 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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122A PHE* 3.0 16.8 + - + +
123A GLU* 4.5 0.4 - - - -
125A ALA* 1.3 76.9 - - - +
127A LYS* 1.3 59.7 + - - +
128A THR 3.5 0.2 + - - -
129A ARG* 3.6 8.1 + - - +
135A ALA* 3.7 19.4 - - + +
172A VAL* 4.2 2.5 - - + -
174A VAL* 4.0 11.0 - - + +
187A ARG* 2.8 26.5 + - - -
191A LEU* 3.5 36.1 - - + -
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Residues in contact with LYS 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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120A GLN* 5.7 4.4 + - - +
123A GLU* 2.8 35.8 + - - +
124A ASP* 3.3 27.9 + - - +
126A ALA* 1.3 77.7 - - - +
128A THR* 1.3 64.0 + - + +
129A ARG 3.6 1.6 + - - +
187A ARG* 3.9 14.5 + - - +
188A PRO* 3.9 32.7 - - + +
191A LEU* 3.7 15.3 - - + -
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Residues in contact with THR 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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124A ASP* 2.7 25.9 + - + +
125A ALA* 3.4 11.6 + - - -
126A ALA 3.3 0.2 - - - -
127A LYS* 1.3 80.4 - - + +
129A ARG* 1.3 60.3 + - - +
130A PHE* 3.1 12.4 + - - +
148A SER* 5.6 0.2 - - - -
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Residues in contact with ARG 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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125A ALA 3.3 17.1 + - - +
126A ALA* 3.8 8.7 - - - +
127A LYS 3.3 2.6 - - - +
128A THR* 1.3 73.6 - - - +
130A PHE* 1.3 72.4 + - - +
131A GLY 3.6 3.5 + - - +
132A SER 3.8 11.7 - - - -
133A GLY* 4.0 5.8 - - - +
134A TRP 4.3 2.0 - - - +
148A SER* 3.0 41.0 + - - +
149A THR* 3.2 25.9 + - - +
150A ALA* 3.5 24.0 - - - +
174A VAL* 3.9 20.6 - - + -
187A ARG* 2.9 26.0 + - - -
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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