Contacts of the strand formed by residues 138 - 144 (chain D) in PDB entry 4BR6
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 LEU 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASN* 3.0 26.9 + - - -
96D LEU* 4.9 3.1 - - + +
99D ALA* 3.6 31.0 - - + +
100D ILE* 3.7 21.8 - - + +
103D ASP* 3.0 24.2 + - - +
104D PHE* 3.8 17.9 - - + -
129D LEU* 4.3 7.2 - - + -
130D ALA 3.4 7.0 - - - +
131D LYS* 4.0 2.7 - - + -
136D GLY 3.8 13.5 - - - +
137D ASN* 1.3 74.9 + - - +
139D ALA* 1.3 61.9 + - - +
156D LEU* 3.6 31.2 - - + -
194D PHE* 4.1 9.0 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ASN* 5.2 1.3 - - - +
139A ALA* 5.9 6.7 - - + -
104D PHE* 4.1 6.7 - - - -
128D TRP 3.7 1.0 - - - +
129D LEU* 3.7 3.6 - - - +
130D ALA* 3.0 33.5 + - + +
137D ASN* 5.1 1.6 - - - +
138D LEU* 1.3 78.1 - - - +
140D ILE* 1.3 65.0 + - - +
141D VAL* 3.9 15.8 + - + -
153D LEU* 5.0 11.9 - - + -
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Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.5 32.7 - - + -
110D PHE* 3.7 21.5 - - + -
113D GLN* 3.6 30.1 - - + +
114D MET* 3.7 22.2 - - - +
117D ALA* 3.7 28.9 - - + -
127D ALA* 5.4 0.7 - - + -
128D TRP 3.4 7.6 - - - +
139D ALA* 1.3 73.5 - - - +
141D VAL* 1.3 70.3 + - - +
142D THR* 5.4 0.2 - - + -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ALA* 3.4 4.0 - - - +
128D TRP* 2.7 53.9 + - + +
130D ALA* 4.3 10.8 - - + -
139D ALA* 4.5 12.8 - - + -
140D ILE* 1.3 80.5 - - - +
142D THR* 1.3 63.2 + - - +
143D ARG* 4.0 15.7 - - - +
149D VAL* 4.1 15.7 - - + -
153D LEU* 4.0 23.1 - - + -
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Residues in contact with THR 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ALA* 3.9 35.2 - - + +
121D ILE* 4.1 14.9 - - + +
126D TRP 3.1 11.2 - - - +
127D ALA* 4.2 4.3 - - + -
128D TRP* 5.2 0.2 - - - -
140D ILE* 5.4 0.2 - - + -
141D VAL* 1.3 79.2 - - - +
143D ARG* 1.3 87.5 + - - +
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 5.1 2.6 - - - +
125D GLY* 3.2 4.5 - - - -
126D TRP* 2.7 42.4 + - + +
128D TRP* 4.1 15.7 - - + -
141D VAL* 4.0 13.3 - - - +
142D THR* 1.3 102.2 + - - +
144D ALA* 1.3 59.2 + - - +
147D ASP* 3.1 35.2 - - - +
148D PRO 2.8 28.3 + - - +
149D VAL* 4.3 13.4 - - + +
150D THR 5.2 3.0 + - - +
153D LEU* 4.0 24.5 - - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ILE* 6.1 1.6 - - - -
124D SER 3.8 5.8 - - - +
143D ARG* 1.3 71.5 - - - +
145D ASN* 1.3 82.4 + - - +
147D ASP* 2.9 34.4 + - - +
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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