Contacts of the helix formed by residues 130 - 138 (chain A) in PDB entry 6W01
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 GLY 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A VAL 3.4 0.6 + - - -
129A ASP* 1.3 71.9 - - - +
131A GLN* 1.3 59.1 + - - +
132A VAL 3.4 2.4 - - - +
133A ASP* 3.3 16.4 + - - +
134A LEU* 2.9 33.9 + - - +
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Residues in contact with GLN 131 (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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82A ALA* 3.3 38.8 + - - +
83A ASN* 4.3 10.5 + - - +
123A PHE 4.5 0.3 - - - +
124A PHE* 3.4 14.9 - - + +
125A ASP* 2.7 54.8 + - - +
128A VAL* 3.2 35.2 + - + +
129A ASP 4.2 1.6 - - - +
130A GLY* 1.3 76.6 - - - +
132A VAL* 1.3 65.4 + - - +
134A LEU* 3.2 17.1 + - + +
135A PHE* 2.9 23.6 + - - +
143A LEU* 4.8 0.7 - - - -
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Residues in contact with VAL 132 (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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126A GLY* 3.7 27.8 - - - +
128A VAL 4.6 1.2 + - - -
130A GLY 3.4 0.8 - - - +
131A GLN* 1.3 75.5 - - - +
133A ASP* 1.3 62.2 + - - +
135A PHE* 3.2 5.2 + - - +
136A ARG* 2.9 40.4 + - + +
143A LEU* 4.1 18.6 - - + -
145A THR* 4.1 11.9 - - + -
149A VAL* 4.1 27.1 - - + -
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Residues in contact with ASP 133 (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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130A GLY* 3.3 15.7 + - - +
131A GLN 3.2 0.4 - - - -
132A VAL* 1.3 77.8 - - - +
134A LEU* 1.3 64.9 + - - +
136A ARG* 3.2 25.2 + - - +
137A ASN* 3.2 32.6 + - - +
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Residues in contact with LEU 134 (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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83A ASN* 5.5 1.1 - - - +
111A LYS* 6.4 0.4 - - + -
112A PRO* 4.1 26.0 - - + -
113A THR* 3.7 31.3 - - + +
124A PHE* 3.5 18.0 - - + -
130A GLY* 2.9 19.9 + - - +
131A GLN* 3.2 24.9 + - + +
133A ASP* 1.3 75.6 - - + +
135A PHE* 1.3 57.2 + - - +
137A ASN* 3.2 6.3 + - + +
138A ALA* 2.9 28.4 + - - +
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Residues in contact with PHE 135 (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 PHE* 3.9 30.0 - + + -
131A GLN 2.9 12.9 + - - +
132A VAL 3.3 8.7 - - - +
134A LEU* 1.3 76.4 - - - +
136A ARG* 1.3 67.6 + - + +
138A ALA* 3.0 12.4 + - + +
141A GLY* 3.6 28.7 - - - -
143A LEU* 3.5 38.6 - - + -
152A LEU* 4.0 25.4 - - + -
180A TYR* 3.9 22.4 - - + -
181A LYS 4.0 5.8 - - - -
182A LYS* 3.1 46.3 + - + +
187A VAL* 5.1 3.1 - - + -
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Residues in contact with ARG 136 (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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132A VAL* 2.9 25.5 + - + +
133A ASP* 3.2 30.7 + - - +
135A PHE* 1.3 82.4 - - + +
137A ASN* 1.3 61.3 + - - +
149A VAL* 3.3 20.6 - - - +
150A LYS* 2.7 40.0 + - - +
151A GLY* 5.4 0.8 - - - -
152A LEU* 4.4 17.1 - - + +
182A LYS* 2.9 17.0 + - - +
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Residues in contact with ASN 137 (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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113A THR* 5.6 9.9 - - + -
133A ASP* 3.2 21.3 + - - +
134A LEU* 3.5 5.8 - - + +
135A PHE 3.1 0.4 - - - -
136A ARG* 1.3 82.1 + - - +
138A ALA* 1.3 63.1 + - - +
139A ARG 3.8 1.0 + - - -
182A LYS* 4.1 0.9 - - - -
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Residues in contact with ALA 138 (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 PRO 6.0 1.8 - - - +
122A VAL* 5.7 0.9 - - + -
124A PHE* 3.6 30.1 - - + -
134A LEU 2.9 16.0 + - - +
135A PHE* 3.0 6.3 + - + +
137A ASN* 1.3 78.1 - - - +
139A ARG* 1.3 61.3 - - - +
140A ASN 4.0 10.5 - - - +
141A GLY* 5.3 0.4 - - - -
182A LYS* 2.6 34.2 + - + +
185A GLY* 4.6 0.5 - - - -
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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