Contacts of the strand formed by residues 146 - 154 (chain A) in PDB entry 3LZR
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 PHE 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.8 24.2 - - + -
13A ASN* 3.4 23.1 - - - +
15A MET* 3.8 8.1 - - + -
17A ILE* 3.4 34.5 - - + -
120A TYR* 3.6 5.8 - - - +
121A ILE* 3.1 53.4 + - + -
143A PHE* 3.6 33.7 - + - -
144A GLU 3.3 4.5 + - - +
145A PRO* 1.3 75.4 - - - +
147A LYS* 1.3 81.7 + - - +
148A VAL* 3.8 6.5 - - + -
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Residues in contact with LYS 147 (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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12A LEU* 4.8 2.8 - - - +
118A THR* 4.0 11.9 - - + -
119A PHE 3.2 16.2 - - - +
120A TYR* 3.8 28.7 - - + +
146A PHE* 1.3 84.7 - - - +
148A VAL* 1.3 68.7 + - - +
149A ASP* 4.1 16.2 - - - +
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Residues in contact with VAL 148 (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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10A LYS* 4.1 17.0 - - + -
12A LEU* 3.8 37.7 - - + -
17A ILE* 4.1 10.1 - - + -
117A LEU 3.7 0.7 - - - +
118A THR* 3.4 4.2 - - - -
119A PHE* 3.1 43.5 + - + -
121A ILE* 4.9 0.2 - - + -
146A PHE* 3.8 8.1 - - + -
147A LYS* 1.3 80.1 - - - +
149A ASP* 1.3 64.1 + - - +
150A TYR* 3.6 32.7 - - + +
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Residues in contact with ASP 149 (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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10A LYS* 3.2 27.2 - - - +
117A LEU 3.5 4.5 - - - +
118A THR* 3.5 22.1 - - - +
147A LYS* 4.1 18.6 - - - +
148A VAL* 1.3 78.8 - - - +
150A TYR* 1.3 63.7 + - - +
151A LYS* 5.7 6.5 - - - +
300A SO4 3.4 7.7 + - - +
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Residues in contact with TYR 150 (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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6A ILE* 3.5 36.3 - - + +
8A ASP 3.3 28.9 - - - -
9A PRO* 4.4 0.2 - - + -
10A LYS* 4.1 5.3 + - + -
17A ILE* 2.7 46.0 + - - +
19A ALA* 4.2 10.3 - - + -
116A GLU* 3.4 8.0 - - - +
117A LEU* 2.7 52.0 + - + +
119A PHE* 3.4 29.0 - + - -
148A VAL* 3.6 21.0 - - + +
149A ASP* 1.3 76.5 - - - +
151A LYS* 1.3 66.6 + - - +
152A PHE 4.4 0.2 - - - -
300A SO4 3.6 8.1 - - - +
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Residues in contact with LYS 151 (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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7A GLY* 3.2 21.1 + - - -
115A TYR 3.5 6.5 - - - +
116A GLU* 4.0 32.2 + - + +
149A ASP* 5.7 6.3 - - - +
150A TYR* 1.3 79.9 + - - +
152A PHE* 1.3 61.6 + - - +
300A SO4 3.1 24.0 + - - +
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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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5A PRO 4.7 3.8 - - - +
6A ILE* 3.6 38.4 - - + -
7A GLY 3.9 15.7 - - - +
21A TYR* 4.0 21.8 - + - -
41A ILE* 5.8 4.3 - - + -
43A LEU* 6.1 0.4 - - + -
72A LEU* 3.8 24.0 - - + -
102A MET* 5.2 4.5 - - + -
114A ASN* 3.8 3.4 - - - +
115A TYR* 2.9 58.9 + + + +
117A LEU* 4.3 9.9 - - + -
151A LYS* 1.3 75.3 - - - +
153A LYS* 1.3 69.9 + - - +
154A TYR* 3.9 22.7 - + + -
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Residues in contact with LYS 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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4A VAL* 5.5 3.3 - - - +
21A TYR* 4.4 4.0 + - - -
112A VAL* 4.9 10.1 - - - +
113A GLY* 3.6 17.5 - - - +
114A ASN* 3.9 24.1 + - - +
152A PHE* 1.3 81.6 - - - +
154A TYR* 1.3 63.2 + - - +
155A THR* 3.3 26.8 + - + +
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Residues in contact with TYR 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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21A TYR* 3.6 19.7 - + - -
40A ASP* 3.8 2.6 - - - +
41A ILE* 3.5 30.7 - - + +
102A MET* 3.6 30.1 - - + -
103A GLU* 2.7 31.9 + - - -
111A GLY 3.7 18.2 - - - -
112A VAL* 3.2 25.1 - - - +
113A GLY 2.9 13.9 + - - +
115A TYR* 3.7 21.5 - - + -
152A PHE* 3.9 14.0 + + + -
153A LYS* 1.3 70.3 - - - +
155A THR* 1.3 58.5 - - - +
156A GLY* 3.5 25.1 - - - -
157A THR* 3.0 19.1 + - - -
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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