Contacts of the strand formed by residues 130 - 136 (chain A) in PDB entry 1LA5
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 TRP 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PRO* 3.5 3.1 - - - +
121A CYS* 3.3 6.9 - - - -
122A ASP* 2.9 39.8 + - + +
125A THR* 3.0 42.0 + - - +
126A GLU* 3.8 13.2 - - - +
128A GLY 3.7 5.4 - - - -
129A GLY* 1.3 78.3 - - - +
131A LEU* 1.3 59.3 + - - +
178A GLU* 4.0 8.1 - - + -
180A ARG* 3.5 35.9 - - + -
194A HIS* 4.1 19.3 - + - -
297A MET* 3.6 39.0 - - + -
298A LEU 3.4 10.8 - - - -
299A ARG* 3.3 61.7 - - + +
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Residues in contact with LEU 131 (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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79A ASP* 5.1 3.1 - - + -
80A PRO* 3.0 39.6 - - + +
96A LEU* 3.6 10.3 - - + -
119A VAL* 2.9 38.4 - - + -
120A PHE 3.9 0.7 - - - -
130A TRP* 1.3 70.5 - - - +
132A VAL* 1.3 63.9 + - - +
133A PHE* 3.4 5.0 + - + +
163A LEU* 4.8 12.1 - - + -
168A LEU* 5.9 2.9 - - + -
171A LEU* 2.9 32.8 - - + -
297A MET* 3.2 1.5 - - - -
298A LEU* 2.8 52.1 + - + +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 3.7 13.2 - - - +
120A PHE* 2.7 70.8 + - + +
122A ASP* 4.6 3.1 - - + -
130A TRP 3.8 0.2 + - - -
131A LEU* 1.3 71.3 - - - +
133A PHE* 1.3 59.6 + - - +
134A GLN 4.6 5.8 - - - +
135A ARG* 4.3 9.0 - - + +
161A PHE* 3.5 21.0 - - + -
163A LEU* 5.0 1.4 - - - +
296A MET 3.5 6.1 - - - +
297A MET* 3.2 39.0 - - + -
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Residues in contact with PHE 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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131A LEU* 3.4 4.7 + - + +
132A VAL* 1.3 73.3 - - - +
134A GLN* 1.4 59.4 + - - +
161A PHE* 3.2 6.1 - - - -
162A TRP* 3.9 23.8 - + + -
163A LEU* 3.0 47.4 + - + -
168A LEU* 4.0 28.0 - - + -
179A LEU* 4.5 15.0 - - + -
181A VAL* 6.4 0.2 - - + -
198A PHE* 4.6 20.9 - + - -
254A TRP* 5.7 0.7 - + - -
296A MET* 2.9 70.1 + - + -
297A MET* 3.6 17.5 - - - -
298A LEU* 4.3 7.0 - - + -
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Residues in contact with GLN 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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132A VAL* 3.6 2.2 - - - +
133A PHE* 1.4 78.6 - - - +
135A ARG* 1.4 81.7 + - - +
136A ARG* 3.2 26.7 - - - +
143A PHE* 4.8 2.0 - - + -
161A PHE* 3.3 20.2 - - - +
162A TRP* 3.6 26.0 - - + -
253A TRP* 5.3 0.2 - - - -
263A LEU* 3.5 16.0 + - - +
264A ASN* 3.1 21.4 + - - +
294A VAL* 3.8 8.7 - - - +
295A ARG* 4.1 0.2 - - - +
296A MET* 2.9 55.0 + - + +
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Residues in contact with ARG 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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120A PHE* 2.9 46.4 - - - +
132A VAL* 4.4 5.7 - - + +
134A GLN* 1.4 83.7 + - - +
136A ARG* 1.4 67.7 + - - +
137A GLN* 6.3 0.4 - - + -
143A PHE* 4.1 3.3 - - - -
157A GLN 2.7 19.6 + - - -
158A GLU* 3.8 10.4 + - - +
159A SER 2.6 34.9 + - - +
160A GLU* 3.2 7.3 - - - +
161A PHE* 3.1 40.0 + - - +
294A VAL 3.4 2.0 - - - -
295A ARG* 3.0 40.6 - - + +
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Residues in contact with ARG 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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134A GLN* 3.2 15.5 - - - +
135A ARG* 1.4 75.5 - - - +
137A GLN* 1.4 65.7 + - - +
140A SER 3.7 10.1 + - - +
143A PHE* 3.3 44.2 - - - -
160A GLU* 4.3 6.5 + - - -
263A LEU 3.0 16.9 + - - +
264A ASN* 4.1 2.6 - - - -
265A GLY 2.7 24.8 + - - +
267A TYR* 3.7 29.0 - - + +
279A ILE* 3.0 27.8 - - + +
291A TYR 5.5 1.3 - - - +
292A ARG 4.2 4.7 - - - +
293A ARG* 3.4 21.5 - - - +
294A VAL* 3.0 38.4 + - + +
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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