Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 1SAW
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 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 1.3 74.7 - - - +
148A LEU* 1.3 65.8 + - - +
159A GLU* 6.5 0.9 - - + -
160A GLY 3.7 9.2 - - - +
161A GLU* 4.3 15.0 - - + -
209A ILE* 3.4 7.7 - - - +
210A HIS* 3.1 56.4 + - + +
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Residues in contact with LEU 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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27A TYR* 4.2 11.4 - - - +
72A LEU* 3.4 22.0 - - + -
73A GLU* 4.7 5.4 - - - -
74A LEU* 4.3 22.7 - - + +
99A LEU* 4.1 6.7 - - + -
146A LEU* 4.5 2.2 - - + -
147A LYS* 1.3 81.2 - - - +
149A TRP* 1.3 63.1 + - - +
159A GLU* 3.4 6.2 - - - +
160A GLY* 2.9 34.2 + - - +
162A THR* 4.0 30.1 - - + -
193A PRO* 4.9 9.2 - - + -
208A GLY 3.5 3.4 - - - +
209A ILE* 3.6 35.0 - - + -
210A HIS* 5.4 0.3 - - - -
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Residues in contact with TRP 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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72A LEU* 3.3 6.3 - - - +
148A LEU* 1.3 77.3 - - - +
150A LEU* 1.3 70.8 + - - +
151A LYS* 4.1 23.1 - - + -
156A LEU* 4.3 13.0 - - + -
158A GLN 3.2 9.6 - - - +
159A GLU* 4.3 5.2 - - + -
206A GLU* 3.5 41.7 - - + -
207A ALA* 3.2 18.7 - - - +
208A GLY* 3.1 54.7 + - - -
209A ILE 4.3 0.8 - - - -
210A HIS* 3.3 52.3 + + - +
213A VAL 5.0 0.6 + - - -
214A SER* 4.4 13.2 - - - -
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Residues in contact with LEU 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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70A HIS* 3.2 45.1 - - + +
72A LEU* 4.1 6.5 - - + +
101A LEU* 3.8 23.3 - - + -
149A TRP* 1.3 79.5 - - - +
151A LYS* 1.3 78.9 + - - +
152A VAL* 3.8 8.7 - - + -
156A LEU* 3.8 3.9 - - - +
157A ARG* 3.0 27.4 + - + -
158A GLN* 2.9 28.1 + - + +
205A ILE* 3.7 25.4 - - + -
206A GLU 3.3 5.8 - - - +
207A ALA* 4.2 1.1 - - + -
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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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149A TRP* 4.1 23.1 - - + -
150A LEU* 1.3 81.5 - - - +
152A VAL* 1.3 62.1 + - - +
153A ASN 3.9 0.4 - - - -
154A GLY* 3.8 26.1 + - - +
155A GLU 3.2 24.0 - - - +
156A LEU* 4.0 15.7 - - + +
204A GLU 3.6 0.5 - - - +
205A ILE* 3.3 6.9 - - - -
206A GLU* 2.7 53.4 + - + +
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Residues in contact with VAL 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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70A HIS* 4.1 6.7 - - + +
150A LEU* 3.8 17.0 - - + -
151A LYS* 1.3 75.9 - - - +
153A ASN* 1.3 90.1 + - - +
155A GLU* 3.1 26.1 + - - +
157A ARG* 3.6 36.0 + - + +
198A PRO 4.9 0.4 - - - +
199A VAL* 3.9 23.3 - - + -
203A ASP* 3.6 19.5 - - + +
204A GLU 3.5 6.1 - - - +
205A ILE* 4.5 3.8 - - + -
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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