Contacts of the strand formed by residues 151 - 154 (chain A) in PDB entry 3LAW
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 TYR 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.3 39.6 - + - -
90A VAL* 4.8 0.3 - - - +
122A VAL* 3.3 22.9 - - + -
124A GLY* 3.6 13.5 - - - -
132A ARG* 4.8 1.0 + - - -
134A VAL 5.7 0.2 + - - -
135A ALA 5.0 0.3 + - - -
136A THR* 4.4 11.8 - - + -
139A ALA* 3.8 18.6 - - + +
140A GLN* 4.5 29.1 + - + +
143A CYS* 3.9 20.6 - - + -
149A ILE 4.3 0.4 - - - +
150A PRO* 1.3 77.4 - - - +
152A PHE* 1.3 71.1 + - - +
153A GLU* 2.7 44.3 + - + +
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Residues in contact with PHE 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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121A VAL* 4.1 18.2 - - + -
122A VAL 3.1 4.3 + - - +
123A LEU* 3.5 5.5 - - + -
124A GLY 2.8 31.2 + - - -
150A PRO* 4.1 5.4 - - + -
151A TYR* 1.3 95.1 - - - +
153A GLU* 1.3 58.1 + - - +
154A THR* 3.9 17.4 + - + -
161A ASN* 4.4 9.2 - - + +
164A GLN* 3.9 31.2 - - - -
165A ALA* 3.6 31.9 - - + -
168A THR* 3.4 37.7 - - + -
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Residues in contact with GLU 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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90A VAL* 5.2 0.4 - - - -
124A GLY 3.3 5.8 - - - +
127A ILE* 3.3 27.8 - - + +
132A ARG* 2.9 34.7 + - - -
136A THR* 2.8 37.4 + - + -
151A TYR* 2.7 34.6 + - + +
152A PHE* 1.3 72.0 - - - +
154A THR* 1.3 57.2 + - - +
161A ASN* 2.5 34.4 + - - +
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Residues in contact with THR 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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24A LEU* 3.6 14.5 - - + +
123A LEU* 4.3 19.3 - - + +
124A GLY 2.9 5.3 + - - -
125A ASN* 3.2 24.5 + - - +
126A LYS 2.7 29.1 + - - -
127A ILE* 3.2 11.4 - - - +
152A PHE* 4.0 16.2 - - + +
153A GLU* 1.3 78.4 - - - +
155A SER* 1.3 56.6 + - - +
160A ILE 3.1 8.5 - - - -
161A ASN* 3.5 26.7 - - + +
162A VAL* 4.8 2.7 - - - -
165A ALA* 4.4 1.1 - - + -
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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