Contacts of the helix formed by residues 141 - 153 (chain A) in PDB entry 6C90
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 ASP 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.6 3.5 + - - +
140A LEU* 1.3 78.4 - - - +
142A ALA* 1.3 67.7 + - - +
143A PHE* 3.3 17.9 - - + -
144A GLN* 2.8 15.6 + - - +
145A ARG* 3.1 24.3 + - - +
165A ALA 4.3 6.4 - - - +
311A TYR* 3.3 33.1 + - + -
527A ARG* 4.3 4.7 + - - -
1101A ADP 3.5 19.4 + - - -
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Residues in contact with ALA 142 (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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107A VAL* 4.2 12.3 - - + -
108A GLU 4.2 19.3 - - - +
109A GLY* 4.7 5.4 - - - +
110A CYS* 4.2 13.9 - - - -
141A ASP* 1.3 74.2 - - - +
143A PHE* 1.3 62.8 + - - +
145A ARG* 3.2 29.1 + - - +
146A GLU* 3.0 24.9 + - - +
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Residues in contact with PHE 143 (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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109A GLY 4.7 2.6 + - - +
110A CYS* 3.7 25.5 - - + -
141A ASP* 4.0 16.8 - - + -
142A ALA* 1.3 79.3 - - - +
144A GLN* 1.3 81.0 + - + +
146A GLU* 3.5 0.4 + - - -
147A ALA* 3.0 25.6 + - - +
159A VAL* 4.0 27.8 - - + -
161A ALA* 4.2 7.4 - - + -
165A ALA* 3.3 46.9 - - + -
166A GLY 4.2 7.9 - - - -
167A LYS* 4.5 2.7 - - + -
170A CYS* 4.7 1.1 - - - -
307A ILE* 3.4 22.1 - - + +
309A THR* 3.7 22.4 - - + -
311A TYR* 4.6 7.4 - + - -
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Residues in contact with GLN 144 (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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140A LEU* 3.4 21.4 - - + +
141A ASP* 2.8 32.3 + - - +
143A PHE* 1.3 101.2 - - + +
145A ARG* 1.3 59.9 - - - +
147A ALA* 3.3 1.6 + - - +
148A ILE* 2.8 37.3 + - + +
165A ALA 3.6 7.2 + - - -
166A GLY 3.0 23.7 + - - +
169A VAL* 3.7 14.6 - - + +
170A CYS* 4.2 8.7 - - - -
1101A ADP 3.1 34.9 + - - -
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Residues in contact with ARG 145 (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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107A VAL* 4.3 14.1 - - - +
139A ILE* 4.9 4.6 - - - +
140A LEU* 2.8 48.9 + - + -
141A ASP* 3.1 11.6 + - - +
142A ALA* 3.2 29.9 + - - +
144A GLN* 1.3 75.8 - - - +
146A GLU* 1.3 64.8 + - - +
148A ILE* 3.4 9.6 + - - +
149A GLN* 3.0 23.6 + - - +
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Residues in contact with GLU 146 (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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104A VAL* 4.7 3.8 - - - +
106A THR* 3.7 22.4 - - + +
107A VAL* 6.2 0.2 - - - +
110A CYS* 4.8 4.7 - - - -
112A HIS* 2.9 41.8 + - + +
125A LEU* 5.0 0.5 - - - +
142A ALA 3.0 17.2 + - - +
143A PHE* 3.8 6.1 - - - +
144A GLN 3.2 0.2 - - - -
145A ARG* 1.3 74.0 - - - +
147A ALA* 1.3 66.6 + - - +
149A GLN* 3.1 29.9 + - - +
150A CYS* 3.2 15.6 + - - -
307A ILE* 3.5 16.6 - - + -
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Residues in contact with ALA 147 (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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143A PHE 3.0 17.8 + - - +
144A GLN 3.8 3.8 - - - +
146A GLU* 1.3 75.1 - - - +
148A ILE* 1.3 61.4 + - - +
150A CYS* 3.1 18.8 + - - +
151A VAL* 3.3 11.8 + - - +
157A VAL* 4.3 7.5 - - + +
159A VAL* 3.7 30.3 - - + -
170A CYS* 3.8 16.6 - - + -
307A ILE* 3.9 13.5 - - + +
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Residues in contact with ILE 148 (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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128A ARG* 3.9 9.9 - - - +
136A TYR* 4.3 13.0 - - + +
140A LEU* 3.7 28.5 - - + -
144A GLN 2.8 23.7 + - - +
145A ARG* 3.7 6.3 - - - +
146A GLU 3.2 0.2 - - - -
147A ALA* 1.3 76.7 - - - +
149A GLN* 1.3 59.7 + - - +
151A VAL* 3.1 10.0 + - - +
152A ASP* 2.9 38.9 + - - +
169A VAL* 4.3 8.5 - - + -
170A CYS* 4.7 10.8 - - - -
173A TYR* 3.8 43.7 - - + -
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Residues in contact with GLN 149 (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 LEU* 3.7 24.9 + - + +
126A LYS 3.2 28.6 + - - +
127A PRO* 4.0 5.4 - - - +
128A ARG* 5.3 4.0 - - + +
145A ARG 3.0 13.9 + - - +
146A GLU* 3.1 28.2 + - - +
148A ILE* 1.3 75.5 - - - +
150A CYS* 1.3 63.2 + - - +
152A ASP* 3.2 10.5 + - + +
153A ASN* 2.8 38.4 + - - +
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Residues in contact with CYS 150 (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 HIS* 4.3 6.3 - - - -
125A LEU* 3.8 19.1 - - - -
146A GLU 3.2 13.9 + - - -
147A ALA* 3.1 9.9 + - - +
149A GLN* 1.3 76.9 - - - +
151A VAL* 1.3 62.4 + - - +
153A ASN* 3.1 5.2 + - - +
154A ASN 3.1 4.5 + - - -
155A GLN* 3.0 36.3 + - - +
157A VAL* 3.9 17.5 - - + -
305A HIS* 3.5 39.0 - - + -
307A ILE* 4.7 1.8 - - - -
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Residues in contact with VAL 151 (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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147A ALA 3.3 12.1 + - - +
148A ILE* 3.1 10.1 + - - +
150A CYS* 1.3 75.8 - - - +
152A ASP* 1.3 57.8 + - - +
154A ASN* 2.8 20.4 + - - +
157A VAL* 4.4 5.8 - - + -
170A CYS* 4.9 7.9 - - + +
173A TYR* 4.0 16.6 - - + -
174A ALA* 4.0 17.9 - - + -
177A LEU* 3.7 27.4 - - + +
248A TRP* 3.8 23.5 - - + -
280A VAL* 4.1 25.4 - - + -
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Residues in contact with ASP 152 (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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128A ARG* 2.9 52.7 + - + +
131A LYS 5.5 0.2 - - - +
148A ILE* 2.9 18.6 + - - +
149A GLN* 3.2 14.0 + - + +
151A VAL* 1.3 76.1 - - - +
153A ASN* 1.3 64.0 + - - +
154A ASN* 3.3 8.0 + - - +
173A TYR* 2.5 29.3 + - - -
177A LEU* 4.5 11.4 - - - +
180A ARG* 5.7 1.2 + - - -
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Residues in contact with ASN 153 (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 LEU* 3.7 27.0 - - + +
126A LYS* 3.1 47.8 + - - +
127A PRO 5.7 0.2 - - - -
128A ARG* 5.8 0.2 - - - +
149A GLN* 2.8 35.6 + - - +
150A CYS 3.7 2.7 - - - +
151A VAL 3.1 0.4 - - - -
152A ASP* 1.3 79.8 - - - +
154A ASN* 1.3 71.0 + - - +
155A GLN* 3.3 14.3 + - + +
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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