Contacts of the strand formed by residues 147 - 151 (chain I) in PDB entry 6PST
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 147 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30I ILE* 4.5 16.7 - - - +
31I GLN* 4.1 12.7 + - - -
145I ILE 3.7 1.4 + - - -
146I VAL* 1.3 79.6 - - - +
148I GLN* 1.3 58.4 + - - +
453I ILE* 3.5 15.9 - - - -
454I ARG 3.1 19.0 + - - -
455I SER* 4.3 8.7 - - - +
459I MET* 4.2 0.7 - - - -
527I LYS 4.8 0.9 + - - -
529I ARG 3.3 13.1 + - - -
530I ILE* 3.5 10.4 - - - +
531I SER* 2.9 25.3 + - - -
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Residues in contact with GLN 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I VAL 3.6 1.4 + - - -
147I SER* 1.3 73.7 - - - +
149I LEU* 1.3 70.2 + - - +
150I HIS* 4.0 3.8 - - + -
453I ILE* 2.9 31.6 - - - +
454I ARG* 2.2 53.7 + - + -
459I MET* 3.9 13.4 - - + +
511I LEU* 4.4 16.1 - - + +
530I ILE* 4.4 0.7 - - - -
531I SER 3.4 4.3 - - - +
533I LEU 2.8 29.7 + - - +
534I GLY* 3.4 13.7 - - - -
535I PRO 3.5 5.1 + - - +
536I GLY 4.6 0.2 - - - -
537I GLY* 3.3 24.9 - - - +
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Residues in contact with LEU 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I GLN* 1.3 76.2 - - - +
150I HIS* 1.3 59.4 + - - +
448I LEU* 4.2 19.1 - - + -
451I ARG* 3.4 57.2 + - + +
452I ARG 3.5 4.3 - - - +
453I ILE* 3.9 17.3 - - + -
530I ILE* 3.5 21.1 - - + -
531I SER 2.9 14.9 + - - +
532I ALA* 4.0 22.4 - - + +
537I GLY* 5.1 2.5 - - - -
538I LEU* 5.9 0.7 - - - +
558I VAL* 6.0 2.5 - - + -
573I ASN* 4.0 21.3 - - - +
587I LEU* 5.1 3.6 - - + -
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Residues in contact with HIS 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I GLN* 4.6 4.3 - - - +
149I LEU* 1.3 76.1 - - - +
151I ARG* 1.3 85.7 + - - +
152I SER* 5.0 0.7 - - - -
153I PRO* 5.6 2.9 - - + -
451I ARG* 4.1 4.3 - - - -
452I ARG* 2.9 74.6 + - + +
454I ARG* 3.1 61.3 + - + +
458I GLU* 5.3 0.2 - - - -
536I GLY 4.0 23.1 - - - +
537I GLY* 4.7 4.5 - - - +
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Residues in contact with ARG 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I HIS* 1.3 93.2 + - - +
152I SER* 1.3 64.8 + - - +
153I PRO* 4.5 1.2 - - - +
156I PHE* 3.5 33.2 - - + -
177I ILE* 3.2 33.0 - - - +
183I TRP* 4.3 19.6 - - - -
445I ILE* 6.3 5.2 - - - +
450I ASN* 3.6 10.8 - - + +
451I ARG* 4.2 11.5 - - + +
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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