Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 1LWP
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 ASP 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU* 2.8 42.1 - - + +
117A TYR* 4.6 1.0 - - + +
146A LYS* 3.2 4.7 - - - -
147A ASP* 2.4 47.3 + - - +
148A GLU* 3.4 9.7 - - - +
150A VAL* 1.4 90.0 - - + +
152A TYR* 1.3 65.0 + - + +
153A VAL* 3.8 4.2 + - + -
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Residues in contact with TYR 152 (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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144A MET* 3.5 18.4 - - + -
145A SER 3.4 7.6 - - - +
146A LYS* 4.4 2.5 - - + +
150A VAL 4.0 2.4 + - - -
151A ASP* 1.3 72.5 - - - +
153A VAL* 1.4 71.6 + - - +
190A ALA* 5.6 0.2 - - - -
191A THR* 2.6 39.6 + - + +
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Residues in contact with VAL 153 (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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116A LEU* 4.3 5.6 - - + -
144A MET* 3.7 3.3 - - - +
145A SER* 2.8 38.7 + - - +
147A ASP* 3.2 30.3 - - - +
151A ASP* 4.0 13.5 - - + +
152A TYR* 1.4 84.9 - - - +
154A PRO* 1.3 70.7 - - - +
155A MET* 4.5 1.3 - - + -
177A ASP* 4.2 4.3 - - - +
188A CYS* 3.1 29.2 - - - -
189A ARG 3.3 13.7 - - - +
190A ALA* 5.1 3.4 - - - -
191A THR* 4.3 2.5 - - - +
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Residues in contact with PRO 154 (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 THR* 5.8 4.5 - - + -
142A MET* 4.2 10.1 - - + -
143A ASP 3.4 9.0 - - - +
144A MET* 4.6 2.9 - - - -
153A VAL* 1.3 86.0 - - - +
155A MET* 1.3 63.2 + - - +
187A THR 4.5 0.4 - - - -
188A CYS* 3.5 6.1 - - - -
189A ARG* 2.8 57.5 + - - +
190A ALA 3.0 7.6 - - - +
191A THR* 2.9 42.2 - - - +
192A LEU 4.4 2.2 - - - +
193A ILE* 6.3 1.1 - - + -
234A LEU* 6.4 0.2 - - + -
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Residues in contact with MET 155 (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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128A PRO* 3.0 39.5 - - + -
130A HIS* 4.1 9.4 - - + +
141A TYR 3.8 0.2 - - - +
142A MET* 3.3 5.6 - - - -
143A ASP* 2.5 75.4 + - - +
145A SER* 2.8 38.4 - - - +
147A ASP* 4.8 0.9 - - - +
153A VAL* 4.5 5.2 - - + -
154A PRO* 1.3 78.3 - - - +
156A LEU* 1.3 60.8 + - - +
186A ARG* 5.0 17.9 - - + -
187A THR 3.5 8.1 - - - +
188A CYS* 4.7 8.3 - - + -
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Residues in contact with LEU 156 (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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141A TYR 2.7 24.2 - - - +
142A MET* 2.6 35.4 - - + +
155A MET* 1.3 74.8 - - - +
157A ASP* 1.3 57.5 + - - +
158A MET* 2.3 68.8 + - + -
159A LYS 5.1 0.4 - - - +
185A GLU 3.5 0.9 - - - +
186A ARG* 3.4 4.5 - - - -
187A THR* 2.7 52.0 + - + +
189A ARG* 4.7 8.7 - - - +
245A ASP* 6.1 0.7 - - - -
248A LEU* 4.6 10.1 - - + -
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Residues in contact with ASP 157 (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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140A GLY* 2.8 25.1 - - - -
141A TYR* 2.8 18.4 + - + +
143A ASP* 5.4 0.4 + - - -
155A MET 4.1 0.8 + - - -
156A LEU* 1.3 70.2 - - - +
158A MET* 1.4 63.2 + - - +
184A PRO* 3.1 23.1 - - - +
185A GLU 3.2 10.0 - - - +
186A ARG* 3.6 34.2 + - + +
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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