Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 6O81
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.4 15.8 - - - -
129A ARG* 1.3 80.1 + - - +
131A LEU* 1.3 60.6 + - - +
132A GLY* 3.3 2.0 + - - -
133A ASP* 3.3 19.1 + - - +
134A VAL* 3.1 28.8 + - - +
267A GLN* 2.3 60.5 + - - +
268A THR* 4.4 2.7 - - - +
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Residues in contact with LEU 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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48A VAL* 3.8 24.0 - - + -
52A PHE* 3.7 10.8 - - + -
130A SER* 1.3 74.3 + - - +
132A GLY* 1.3 60.6 + - - +
134A VAL* 3.2 10.4 + - - +
135A LEU* 2.9 47.1 + - + +
150A LEU* 4.4 20.4 - - + -
152A TYR* 3.4 42.8 - - + +
260A PHE* 4.6 7.2 - - + -
267A GLN 3.8 4.0 + - - +
268A THR* 4.5 8.5 - - + +
269A ARG* 4.5 21.1 - - + +
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Residues in contact with GLY 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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130A SER* 4.4 0.2 - - - -
131A LEU* 1.3 77.3 - - - +
133A ASP* 1.3 57.6 + - - +
135A LEU* 3.8 1.7 - - - +
136A ARG* 2.9 43.1 + - - +
260A PHE* 3.6 33.9 - - - +
266A TYR 4.4 1.8 - - - -
267A GLN 3.2 14.3 + - - -
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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
----------------------------------------------------------
127A LEU 5.5 0.2 - - - +
128A TYR* 3.7 19.0 - - + -
129A ARG* 3.7 8.2 + - - +
130A SER* 3.3 32.1 + - - +
131A LEU 3.2 0.2 - - - -
132A GLY* 1.3 74.6 - - - +
134A VAL* 1.3 59.5 + - - +
136A ARG* 2.5 37.9 + - + +
137A ASP* 2.9 37.7 + - - +
267A GLN* 4.5 4.2 - - - +
430T THR* 6.1 0.7 - - - -
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Residues in contact with VAL 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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46A VAL* 5.6 4.3 - - + -
48A VAL* 4.4 17.5 - - + -
52A PHE* 4.5 7.9 - - + -
94A PHE* 3.5 40.4 - - + -
128A TYR* 3.7 28.7 - - + -
130A SER 3.1 15.3 + - - +
131A LEU* 3.2 13.0 + - - +
133A ASP* 1.3 75.5 - - - +
135A LEU* 1.3 63.1 + - + +
137A ASP* 3.3 9.1 + - - +
138A VAL* 2.9 28.9 + - + +
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Residues in contact with LEU 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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46A VAL* 4.4 12.8 - - + -
131A LEU* 2.9 31.3 + - + +
132A GLY 3.9 3.8 - - - +
134A VAL* 1.3 79.5 - - + +
136A ARG* 1.3 58.7 + - - +
138A VAL* 3.3 14.0 + - + +
139A ASP 2.9 21.3 + - - -
148A PHE* 3.9 30.5 - - + -
150A LEU* 4.7 13.5 - - + -
181A MET* 6.3 0.7 - - + -
256A VAL* 4.5 12.3 - - + -
257A ALA* 3.5 17.2 - - + +
260A PHE* 3.6 39.7 - - + -
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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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130A SER* 5.8 0.2 - - - -
132A GLY* 2.9 16.6 + - - +
133A ASP* 2.5 61.4 + - - +
135A LEU* 1.3 73.5 - - - +
137A ASP* 1.3 66.4 + - - +
139A ASP* 3.4 1.9 + - - +
140A ALA* 2.9 28.1 + - - +
257A ALA 4.8 0.9 - - - -
260A PHE* 2.5 37.1 + - - +
261A THR* 3.8 28.1 - - + +
263A ASN 3.5 11.5 + - - -
264A PHE* 3.7 36.5 + - - +
266A TYR 4.3 3.2 + - - -
267A GLN* 5.8 1.0 + - - -
430T THR* 4.9 12.5 - - - -
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Residues in contact with ASP 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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94A PHE* 4.6 9.9 - - + -
128A TYR* 3.6 30.5 - - - +
133A ASP* 2.9 24.1 + - - +
134A VAL* 3.3 5.2 + - - +
136A ARG* 1.3 78.7 - - - +
138A VAL* 1.3 60.8 + - - +
140A ALA* 3.8 7.0 - - - +
141A LYS* 2.9 53.7 + - - +
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Residues in contact with VAL 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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46A VAL* 4.2 14.6 - - + -
94A PHE* 3.6 28.0 - - + -
134A VAL* 2.9 20.7 + - + +
135A LEU* 3.3 19.7 + - + +
137A ASP* 1.3 76.8 - - - +
139A ASP* 1.3 58.2 + - - +
141A LYS 3.4 0.3 + - - -
142A ALA* 2.8 28.2 + - - -
143A LEU* 3.5 15.3 + - + -
144A VAL* 4.2 36.8 - - + +
148A PHE* 5.2 1.8 - - + -
257A ALA* 4.9 7.2 - - + -
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Residues in contact with ASP 139 (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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135A LEU 2.9 16.0 + - - +
136A ARG 3.7 4.9 - - - +
137A ASP 3.3 0.2 - - - -
138A VAL* 1.3 76.7 - - - +
140A ALA* 1.3 60.0 + - - +
142A ALA* 3.5 7.8 + - - +
254A PRO 4.5 0.7 - - - +
257A ALA* 3.7 21.4 - - + +
258A GLN* 2.8 38.9 + - - +
261A THR* 3.5 26.6 + - + +
75T ARG* 4.0 5.4 + - - -
352T ARG* 2.9 35.0 + - - -
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Residues in contact with ALA 140 (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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136A ARG 2.9 17.7 + - - +
137A ASP* 3.9 9.2 - - - +
139A ASP* 1.3 76.9 - - - +
141A LYS* 1.3 65.0 + - + +
142A ALA* 5.0 0.3 - - - +
261A THR* 5.5 0.4 - - + +
301T VAL 5.3 11.8 - - - +
352T ARG* 4.6 6.4 + - - +
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Residues in contact with LYS 141 (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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94A PHE* 5.5 1.7 - - + -
123A ILE* 4.4 27.9 - - + +
137A ASP* 2.9 37.9 + - - +
140A ALA* 1.3 78.3 - - + +
142A ALA* 1.3 69.4 + - - +
143A LEU* 3.8 35.4 - - + +
303T LYS* 4.5 29.6 + - - +
304T ALA* 5.8 2.0 - - - +
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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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138A VAL 2.8 13.0 + - - -
139A ASP* 3.5 10.0 + - - +
140A ALA 3.4 2.3 - - - +
141A LYS* 1.3 80.7 - - - +
143A LEU* 1.3 60.9 + - - +
144A VAL* 3.7 3.4 - - - -
145A ARG* 3.3 27.8 + - - +
352T ARG* 4.8 13.5 - - - +
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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