Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 3DC6
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 ILE 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ASP* 3.6 23.8 - - - +
127A TYR* 3.7 7.3 - - - -
128A CYS* 2.9 27.4 + - + +
131A GLY* 3.4 19.7 - - - +
132A LYS* 1.3 85.9 - - - +
134A LEU* 1.3 69.8 + - - +
135A LYS* 4.1 25.8 - - + -
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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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92A LEU* 4.2 5.4 - - + -
95A ALA* 3.6 38.4 - - + +
96A ILE* 3.6 22.4 - - + +
99A ASP* 2.8 21.3 + - - +
100A PHE* 3.6 24.9 - - + -
125A LEU* 4.2 8.1 - - + -
126A GLY 3.3 6.3 - - - +
127A TYR* 4.1 5.8 - - + -
133A ILE* 1.3 80.1 - - - +
135A LYS* 1.3 65.3 + - - +
154A LEU* 3.5 31.4 - - + -
192A PHE* 3.9 18.6 - - + -
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Residues in contact with LYS 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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100A PHE* 4.1 6.5 - - - -
125A LEU* 3.6 3.2 - - - +
126A GLY* 2.8 39.4 + - - +
128A CYS* 3.8 23.0 - - - -
131A GLY* 6.1 0.4 - - - -
133A ILE* 4.1 27.8 - - + +
134A LEU* 1.3 82.4 - - - +
136A VAL* 1.3 66.8 + - - +
137A ALA 4.0 0.3 + - - -
151A LEU* 3.9 32.8 - - + +
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Residues in contact with VAL 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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100A PHE* 3.8 19.9 - - + -
106A LEU* 4.1 6.3 - - + -
109A GLN* 3.8 23.5 + - - +
110A LEU* 3.7 46.0 - - + +
113A SER* 3.7 29.2 - - - +
124A TRP 3.4 4.0 - - - +
125A LEU* 5.1 1.3 - - + -
135A LYS* 1.3 77.2 - - - +
137A ALA* 1.3 65.6 + - - +
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Residues in contact with ALA 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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124A TRP* 2.8 36.9 + - + +
126A GLY 6.1 0.2 - - - +
135A LYS 4.0 0.6 + - - +
136A VAL* 1.3 77.8 - - - +
138A THR* 1.3 70.2 + - - +
145A LEU* 3.9 17.7 - - + -
149A THR* 5.6 3.4 - - + -
151A LEU* 3.8 26.5 - - + -
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Residues in contact with THR 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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113A SER* 3.6 40.6 - - - +
117A VAL* 3.8 15.5 - - + +
122A TRP 3.2 13.9 - - - +
123A GLY* 4.3 5.6 - - - -
124A TRP* 5.1 0.2 - - - -
136A VAL* 5.4 0.7 - - + -
137A ALA* 1.3 81.9 - - - +
139A CYS* 1.3 67.9 - - - +
149A THR* 5.7 2.4 - - - +
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Residues in contact with CYS 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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117A VAL* 4.8 4.5 - - - +
121A GLY* 3.2 5.2 - - - -
122A TRP* 3.0 34.9 + - + +
124A TRP* 3.8 16.2 - - - +
138A THR* 1.3 79.5 - - - +
140A ALA* 1.3 59.3 + - - +
141A ASN 4.5 0.2 - - - +
143A ASP* 3.2 29.4 - - + +
144A PRO 4.5 0.9 - - - -
145A LEU* 3.7 37.2 - - - -
148A THR* 4.6 7.0 - - - -
149A THR* 5.0 3.4 - - - -
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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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117A VAL* 5.7 1.8 - - - -
120A SER 3.9 5.2 - - - +
139A CYS* 1.3 72.7 - - - +
141A ASN* 1.3 80.0 + - - +
143A ASP* 2.9 39.2 + - - +
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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