Contacts of the strand formed by residues 128 - 137 (chain B) in PDB entry 5LAL
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 LYS 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.4 10.8 - - - +
123B ASN* 3.0 33.2 + - - +
124B SER 4.5 5.2 - - - +
127B HIS* 1.3 75.3 - - - +
129B GLY* 1.3 59.3 - - - +
153B GLY* 3.8 2.4 - - - -
154B ASP* 2.8 43.5 + - - +
155B PHE* 5.0 0.4 - - - -
1F NAG 4.1 19.8 + - - +
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Residues in contact with GLY 129 (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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121B VAL* 4.7 0.3 - - - +
122B PHE* 2.9 34.4 + - - +
128B LYS* 1.3 77.2 - - - +
130B THR* 1.3 69.4 + - - +
152B THR* 3.2 15.3 - - - -
153B GLY* 4.0 5.4 - - - -
154B ASP 4.1 0.4 - - - -
155B PHE* 4.1 8.1 - - - -
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Residues in contact with THR 130 (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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119B THR* 3.5 21.3 - - + +
120B LEU 3.1 11.2 - - - +
121B VAL* 4.4 14.1 - - + -
122B PHE* 4.7 0.2 - - - -
129B GLY* 1.3 80.1 - - - +
131B LEU* 1.3 62.7 + - - +
132B ASN* 4.1 7.3 + - - -
151B GLY* 3.0 4.2 - - - -
152B THR* 2.7 57.3 + - - +
155B PHE* 3.4 10.2 - - - +
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Residues in contact with LEU 131 (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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43B PHE* 4.7 1.8 - - + -
118B TYR 3.9 0.3 - - - +
119B THR* 3.2 4.2 - - - -
120B LEU* 2.8 46.8 + - + +
122B PHE* 4.1 20.2 - - + -
130B THR* 1.3 74.5 - - - +
132B ASN* 1.3 62.5 + - - +
133B ILE* 4.1 5.3 + - + +
148B VAL* 3.9 14.4 - - + -
150B GLY 3.5 8.1 - - - +
155B PHE* 3.5 42.2 - - + -
158B ALA* 3.8 20.2 - - + -
181B ILE* 3.9 27.6 - - + -
183B LEU* 4.3 4.3 - - + -
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Residues in contact with ASN 132 (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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118B TYR 3.5 3.2 - - - +
119B THR* 2.6 31.6 + - - +
130B THR* 4.1 14.3 + - - -
131B LEU* 1.3 71.0 - - - +
133B ILE* 1.3 61.6 - - - +
148B VAL* 3.4 5.4 - - - +
149B VAL* 2.8 42.8 + - + -
150B GLY* 2.9 22.3 + - - +
151B GLY* 4.8 2.0 - - - +
152B THR* 5.0 5.5 - - - +
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Residues in contact with ILE 133 (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 SER* 3.3 3.6 + - - -
118B TYR* 2.9 77.4 + - + +
120B LEU* 3.7 30.5 - - + -
131B LEU* 4.3 6.3 - - + +
132B ASN* 1.3 83.2 - - - +
134B MET* 1.3 66.7 + - - +
146B LEU* 4.0 12.1 - - + -
147B SER 3.2 9.2 - - - +
148B VAL* 3.9 14.1 - - + -
149B VAL* 4.7 1.1 - - - +
162B ALA* 3.8 15.3 - - + -
181B ILE* 3.9 15.7 - - + -
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Residues in contact with MET 134 (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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115B TRP* 3.8 27.4 - - + -
116B PHE 3.3 11.4 - - - +
117B SER* 3.9 12.1 - - - +
133B ILE* 1.3 78.8 - - - +
135B GLY* 1.3 60.2 + - - +
146B LEU* 4.1 6.1 - - - -
147B SER* 3.0 34.4 + - - -
149B VAL* 4.0 29.8 - - + -
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Residues in contact with GLY 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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115B TRP* 3.6 15.0 - - - -
116B PHE 2.9 31.4 + - - -
134B MET* 1.3 79.8 - - - +
136B ALA* 1.3 65.8 + - - -
137B ASP 3.5 0.3 + - - -
146B LEU* 3.7 14.5 - - - +
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Residues in contact with ALA 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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107B ASP* 5.8 0.9 - - - +
113B ASN* 5.4 1.8 - - - +
114B SER 3.8 3.1 - - - +
115B TRP* 3.7 20.6 - - + +
135B GLY* 1.3 72.7 - - - -
137B ASP* 1.3 59.6 + - - +
138B LEU* 3.7 28.3 + - + +
144B ARG* 5.1 1.6 - - - +
145B ASP 4.0 9.0 + - - +
146B LEU* 3.7 12.5 - - - +
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Residues in contact with ASP 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 ASN* 3.1 8.9 - - - +
114B SER* 2.8 35.7 + - - +
116B PHE* 3.4 20.2 - - + -
135B GLY 3.5 1.6 + - - -
136B ALA* 1.3 69.0 - - - +
138B LEU* 1.3 53.9 + - - +
139B MET* 2.8 16.5 + - - +
144B ARG* 2.7 36.1 + - - +
146B LEU* 4.4 5.8 - - + -
164B PHE* 3.6 17.8 - - + -
218B GLY 2.5 33.8 + - - -
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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