Contacts of the strand formed by residues 133 - 139 (chain B) in PDB entry 4L2A
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 3.9 10.5 - - + +
95B ALA* 3.4 32.5 + - + +
96B ILE* 3.5 34.3 - - + +
99B LYS* 3.2 28.9 + - + +
100B TRP* 3.9 15.5 - - + -
125B LEU* 4.2 19.7 - - + -
126B VAL 3.3 17.9 - - - +
127B LYS* 4.5 0.9 - - - -
128B LEU* 4.9 0.2 - - - +
131B GLY 4.1 0.2 + - - -
132B SER* 1.3 78.6 + - - +
134B ASP* 1.3 63.7 + - - +
153B ILE* 4.5 5.4 - - + -
191B PHE* 3.7 25.8 - - + -
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 3.9 19.0 + - - -
100B TRP* 3.9 8.5 - - - -
125B LEU* 3.5 7.1 - - - +
126B VAL* 2.8 34.0 + - + -
128B LEU* 3.8 34.8 - - + +
133B LEU* 1.3 78.6 - - - +
135B ILE* 1.3 83.8 + - - +
136B VAL* 4.4 7.8 - - + +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TRP* 3.5 25.8 - - + +
106B PHE* 3.8 21.1 - - + -
109B ALA* 3.9 11.9 - - + -
110B LEU* 3.6 33.7 - - + +
113B LYS* 3.7 31.0 + - + -
123B THR* 3.7 24.2 - - + -
124B TRP 3.2 11.9 - - - +
125B LEU* 4.6 0.9 - - + -
134B ASP* 1.3 89.7 + - - +
136B VAL* 1.3 73.0 + - - +
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 4.6 2.9 - - - +
123B THR* 3.7 0.5 - - - -
124B TRP* 2.8 57.7 + - + -
126B VAL* 3.9 25.4 - - + -
128B LEU* 5.7 1.8 - - + -
134B ASP* 4.4 11.7 - - - +
135B ILE* 1.3 82.6 - - - +
137B ASN* 1.3 68.2 + - - +
138B THR* 5.2 3.1 - - + -
144B PRO* 4.8 7.9 - - + -
150B VAL* 5.8 0.7 - - + -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 2.9 53.4 + - - +
116B ASN 4.8 1.0 + - - -
117B ASN* 3.2 30.8 + - - +
122B TRP 3.5 3.1 - - - -
123B THR* 2.7 30.1 + - - +
136B VAL* 1.3 78.2 - - - +
138B THR* 1.3 65.9 + - - +
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ASN* 3.7 2.4 + - - -
121B SER* 2.9 24.5 - - - -
122B TRP* 3.0 21.9 + - - +
124B TRP* 2.8 30.5 + - + +
136B VAL* 5.2 5.2 - - + -
137B ASN* 1.3 78.9 - - - +
139B SER* 1.3 60.5 + - - +
142B ALA* 2.8 41.3 + - + +
143B THR* 4.2 7.2 - - - +
144B PRO* 4.4 5.6 - - + -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASN* 4.4 11.4 + - - -
117B ASN* 5.7 1.1 - - - -
118B PHE 5.2 4.8 + - - -
120B SER 3.8 6.5 + - - -
121B SER* 4.2 2.5 - - - -
138B THR* 1.3 74.6 - - - +
140B ASN* 1.3 81.6 + - - +
141B ALA 3.2 0.7 + - - -
142B ALA* 3.2 21.4 + - - +
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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