Contacts of the strand formed by residues 156 - 159 (chain A) in PDB entry 1SXG
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 SER 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A VAL* 4.9 0.7 - - - -
144A LEU* 3.5 34.1 - - - +
147A SER 4.5 6.5 + - - -
149A GLU* 5.7 1.3 - - - -
154A ILE 3.3 5.9 + - - -
155A PRO* 1.3 77.1 - - - +
157A VAL* 1.3 66.0 + - - +
158A THR* 5.0 4.2 + - - +
304A LEU* 4.5 2.2 - - - +
317A SER 3.0 8.5 + - - +
318A ILE* 4.0 17.3 - - - +
319A VAL* 2.9 27.9 + - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.4 3.4 - - + -
144A LEU 3.1 17.0 + - - +
145A ALA* 3.4 3.7 - - - -
146A ALA 3.0 23.2 + - - -
156A SER* 1.3 77.9 - - - +
158A THR* 1.3 64.8 + - - +
297A ILE* 4.0 20.0 - - + +
300A VAL* 4.0 15.3 - - + -
301A ALA* 3.6 33.0 - - + +
304A LEU* 4.8 2.7 - - + -
319A VAL* 3.1 10.8 - - + +
321A LEU* 3.9 29.4 - - + -
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Residues in contact with THR 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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145A ALA* 4.4 0.4 - - - -
146A ALA* 3.4 6.3 - - - +
147A SER 3.0 45.1 - - - +
148A ILE* 5.2 1.7 - - - -
156A SER* 4.3 5.1 + - - +
157A VAL* 1.3 88.8 - - - +
159A ILE* 1.3 74.1 + - - +
161A TYR* 3.8 11.3 - - + +
297A ILE* 4.3 10.8 - - - -
319A VAL 3.3 4.0 + - - -
320A GLN* 3.1 12.6 + - - +
321A LEU 2.8 22.9 + - - -
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Residues in contact with ILE 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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158A THR* 1.3 84.6 + - - +
160A ASP* 1.3 59.6 + - - +
161A TYR* 3.1 26.7 + - + +
164A ALA* 4.1 16.6 - - + -
274A PHE* 3.9 25.6 - - + -
290A VAL* 4.7 0.4 - - + -
291A VAL 4.7 1.3 - - - +
292A GLN* 3.8 40.2 + - + +
293A PRO* 4.0 12.6 - - + -
297A ILE* 4.6 4.5 - - + -
320A GLN* 3.8 5.9 + - - -
321A LEU 3.3 20.9 - - - +
322A PRO 3.7 12.8 - - - +
323A HIS* 4.1 15.0 - - + -
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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