Contacts of the strand formed by residues 155 - 161 (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 GLU 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LYS* 3.2 3.6 - - - +
152A VAL 3.1 33.8 + - - +
153A ASN 3.3 4.4 - - - +
154A GLY* 1.3 78.9 - - - +
156A LEU* 1.3 63.2 + - - +
157A ARG* 3.4 29.7 - - - +
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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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149A TRP* 4.3 13.2 - - + -
150A LEU 3.8 15.3 - - - +
151A LYS* 4.0 19.5 - - + +
154A GLY 4.2 0.6 + - - -
155A GLU* 1.3 72.7 - - - +
157A ARG* 1.3 64.7 + - - +
158A GLN 4.2 3.8 - - - +
159A GLU* 3.2 46.7 - - + +
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Residues in contact with ARG 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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70A HIS* 4.0 20.5 - - - +
150A LEU* 3.0 12.8 + - + +
152A VAL* 3.6 39.4 + - + +
153A ASN* 5.2 3.2 - - - +
155A GLU* 3.4 34.6 - - - +
156A LEU* 1.3 77.2 - - - +
158A GLN* 1.3 62.6 + - - +
159A GLU 4.2 0.9 + - - -
194A LYS 4.3 0.2 - - - +
195A GLY* 3.5 22.2 - - - +
197A GLY* 6.2 0.2 - - - -
198A PRO* 4.3 14.1 + - - +
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Residues in contact with GLN 158 (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* 3.3 24.2 - - - +
72A LEU* 2.9 33.2 + - + +
149A TRP* 3.2 5.5 - - - -
150A LEU* 2.9 41.2 + - + +
156A LEU* 4.2 0.5 - - - +
157A ARG* 1.3 76.9 - - - +
159A GLU* 1.3 64.1 + - - +
192A THR* 2.9 23.7 + - - -
193A PRO* 3.0 23.5 + - + +
194A LYS 3.4 6.5 + - - +
195A GLY 3.1 26.7 - - - +
196A VAL* 3.4 13.3 - - - +
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Residues in contact with GLU 159 (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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147A LYS* 6.5 1.1 - - + -
148A LEU 3.4 11.0 - - - +
149A TRP* 4.3 4.9 - - + -
156A LEU* 3.2 40.6 - - + +
157A ARG 4.2 1.2 + - - -
158A GLN* 1.3 78.0 - - - +
160A GLY* 1.3 57.9 + - - +
193A PRO* 3.9 11.5 - - - +
194A LYS* 4.1 8.9 + - - +
210A HIS* 5.7 3.9 + - - +
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Residues in contact with GLY 160 (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* 5.3 1.1 - - - -
147A LYS* 3.7 5.5 - - - +
148A LEU* 2.9 36.0 + - - +
159A GLU* 1.3 75.5 - - - +
161A GLU* 1.3 63.9 + - - +
193A PRO* 3.6 26.1 - - - +
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Residues in contact with GLU 161 (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* 3.4 7.7 - - - -
146A LEU 3.5 7.6 - - - +
147A LYS* 4.3 16.2 - - + -
160A GLY* 1.3 77.4 - - - +
162A THR* 1.3 60.3 + - - +
163A SER* 3.1 20.1 + - - +
164A SER* 2.8 30.2 + - - +
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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