Contacts of the strand formed by residues 131 - 140 (chain A) in PDB entry 4OD2
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 ALA 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO* 3.9 14.4 - - + -
125A GLU* 3.5 4.7 - - - -
126A LEU* 3.9 16.4 - - + -
130A LYS* 1.3 80.4 - - - +
132A THR* 1.3 63.9 + - - +
133A LEU* 4.3 2.0 - - + -
179A LEU 3.5 1.9 - - - +
180A SER* 3.6 0.3 - - - -
181A LEU* 2.8 51.4 + - + +
183A PRO 4.4 2.9 - - - -
186A TRP* 4.4 14.6 - - + -
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Residues in contact with THR 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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119A PHE 4.0 1.6 - - - +
120A PRO 4.3 0.2 - - - -
121A PRO* 3.7 20.5 - - - +
125A GLU* 2.6 34.0 + - - +
130A LYS* 5.5 0.2 - - - +
131A ALA* 1.3 74.6 + - - +
133A LEU* 1.3 75.5 + - - +
134A VAL* 3.9 10.1 + - + +
178A TYR* 4.4 13.2 - - + -
179A LEU 3.4 8.5 - - - +
180A SER* 3.6 4.9 + - - +
149B LEU* 4.3 18.1 - - + +
151B LYS* 2.7 30.0 + - - +
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Residues in contact with LEU 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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118A LEU* 4.4 2.2 - - + -
119A PHE 3.3 7.2 - - - +
121A PRO* 4.2 17.7 - - + -
131A ALA* 5.0 1.6 - - + +
132A THR* 1.3 78.8 - - - +
134A VAL* 1.3 62.2 + - - +
135A CYS 4.1 0.7 - - - -
149A TRP* 3.7 28.9 - - + -
177A SER 3.9 0.3 - - - +
178A TYR* 3.4 6.6 - - - -
179A LEU* 3.0 43.6 + - + +
181A LEU* 3.8 25.4 - - + -
186A TRP* 4.4 8.7 - - + -
192A TYR* 3.7 20.9 - - + +
207A VAL* 3.7 29.6 - - + -
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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
----------------------------------------------------------
117A THR 3.4 3.5 - - - +
118A LEU* 3.2 5.1 - - - -
119A PHE* 2.8 47.8 + - + +
132A THR* 4.0 11.4 - - + +
133A LEU* 1.3 78.7 - - - +
135A CYS* 1.3 60.4 + - - +
136A LEU* 3.7 33.2 - - + -
177A SER 3.8 2.0 - - - +
178A TYR* 3.8 27.8 - - + -
132B LEU* 4.7 13.0 - - + -
149B LEU* 4.3 17.3 - - + -
187B SER* 3.8 8.3 - - - +
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Residues in contact with CYS 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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116A VAL* 3.6 25.1 - - - -
117A THR 3.5 2.0 - - - -
118A LEU* 3.6 12.5 - - + +
133A LEU 4.1 0.6 - - - -
134A VAL* 1.3 71.2 - - - +
136A LEU* 1.3 62.7 - - - +
137A ILE* 3.9 10.2 + - - +
149A TRP* 3.6 11.2 - - + -
176A SER* 3.7 2.3 - - - -
177A SER* 2.9 37.9 + - - +
194A CYS* 2.0 49.8 - - - -
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Residues in contact with LEU 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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115A SER 3.2 5.7 - - - +
116A VAL* 3.5 0.5 - - - -
117A THR* 2.8 44.2 + - - +
119A PHE* 4.2 17.5 - - + -
134A VAL* 3.7 30.5 - - + -
135A CYS* 1.3 70.3 - - - +
137A ILE* 1.3 61.6 + - - +
138A SER* 5.2 0.4 + - - -
175A ALA 4.0 1.3 - - - -
176A SER* 3.8 20.0 - - - -
178A TYR* 4.6 0.2 - - - +
132B LEU* 5.7 0.4 - - + -
174B PHE* 3.7 36.8 - - + -
187B SER* 4.2 7.9 - - - -
189B VAL* 3.4 33.9 - - + -
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Residues in contact with ILE 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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114A PRO* 3.7 24.5 - - + -
115A SER 3.4 5.4 - - - +
116A VAL* 4.6 5.4 - - + -
135A CYS* 4.1 15.5 - - - +
136A LEU* 1.3 78.1 - - - +
138A SER* 1.3 66.1 + - - +
140A PHE* 3.6 20.2 - - + -
145A VAL* 5.1 1.6 - - + -
147A VAL* 3.7 28.9 - - + -
174A ALA* 3.3 5.4 - - - +
175A ALA* 2.8 46.3 + - + +
176A SER 5.5 0.2 - - - -
177A SER* 5.2 1.8 - - - -
196A VAL* 3.7 34.1 - - + -
174B PHE* 3.7 4.6 - - - -
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Residues in contact with SER 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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114A PRO* 3.6 2.4 - - - +
115A SER* 2.8 46.2 + - - -
136A LEU 5.2 0.2 + - - -
137A ILE* 1.3 78.0 - - - +
139A ASP* 1.3 72.6 + - - +
140A PHE* 3.3 5.1 + - - -
168A GLN* 3.4 17.5 - - - -
173A TYR 3.3 9.0 - - - -
174A ALA* 3.9 2.0 - - - -
172B HIS* 5.6 0.9 - - - -
174B PHE* 5.0 9.2 - - - -
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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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112A ALA* 3.5 11.4 - - - +
113A ALA 3.5 8.5 - - - +
115A SER* 4.5 12.5 + - - +
138A SER* 1.3 81.4 + - - +
140A PHE* 1.3 56.0 + - - +
168A GLN* 2.9 29.5 + - - +
170A ASN* 3.2 14.4 + - - -
172A LYS* 3.5 28.9 + - + +
173A TYR 2.9 8.7 + - - -
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Residues in contact with PHE 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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112A ALA 3.6 9.9 - - - +
114A PRO* 3.7 20.4 - - + -
137A ILE* 3.6 26.7 - - + -
138A SER 3.6 10.3 - - - -
139A ASP* 1.3 78.9 - - - +
141A TYR* 1.3 61.2 + - - +
142A PRO 3.8 12.1 - - - -
143A GLY* 3.8 12.1 - - - -
145A VAL* 3.7 34.5 - - + -
165A PRO* 4.2 5.8 - - + -
172A LYS* 3.8 1.1 - - - +
173A TYR* 2.7 57.5 + - + +
174A ALA* 3.5 28.9 - - - -
175A ALA* 3.8 3.8 - - + -
198A HIS* 4.1 5.4 - - + +
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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