Contacts of the strand formed by residues 144 - 148 (chain B) in PDB entry 2W3S
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 VAL 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLU* 4.0 12.3 - - + +
142B GLY 4.0 1.5 + - - +
143B PRO* 1.3 72.9 - - - +
145B ILE* 1.3 61.4 + - - +
146B TRP* 3.6 28.7 - - + +
309B ASP* 4.8 2.7 - - - +
312B MET* 3.6 16.9 - - + +
326B ILE 3.6 1.4 - - - +
327B GLU* 3.5 2.3 - - - -
328B SER 2.7 36.4 + - - -
330B ARG* 3.8 31.2 - - - +
611B ARG* 3.9 23.6 - - - +
612B LEU* 5.3 8.7 - - + +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PRO* 3.8 21.4 + - + +
144B VAL* 1.3 81.1 - - - +
146B TRP* 1.3 74.9 + - - +
147B ALA* 5.1 1.3 - - + +
325B ARG* 4.0 22.9 - - - -
326B ILE 3.3 8.3 - - - +
327B GLU* 4.0 30.3 - - + +
612B LEU 4.6 4.3 - - - +
416F GLU* 5.8 3.1 - - - +
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Residues in contact with TRP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B VAL* 3.6 11.0 - - + +
145B ILE* 1.3 85.8 - - - +
147B ALA* 1.3 62.5 + - - +
309B ASP* 3.8 18.8 - - - -
312B MET* 3.4 44.2 - - + +
313B LEU* 3.4 37.7 - - + -
324B LEU 4.1 0.2 - - - +
325B ARG* 3.1 4.0 - - - +
326B ILE* 2.7 48.4 + - + +
404B HIS* 4.6 9.6 - + + -
405B TYR* 5.1 1.3 - - + -
609B TRP* 3.7 19.1 - + - -
611B ARG 3.2 28.2 + - - -
612B LEU 3.6 11.1 + - - -
613B ARG 4.4 4.3 - - - +
614B GLY* 3.5 26.5 - - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ILE* 5.5 1.8 - - + -
146B TRP* 1.3 77.3 - - - +
148B ARG* 1.3 60.0 + - - +
149B GLY 4.2 12.7 + - - +
151B VAL* 5.7 2.0 - - + -
324B LEU 3.2 6.1 - - - +
325B ARG* 3.9 22.2 - - + +
404B HIS* 5.2 3.0 - - - +
615B GLN* 5.3 4.7 + - - -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ALA* 1.3 72.4 - - - +
149B GLY* 1.3 66.0 + - - +
150B ASP 3.7 0.2 + - - -
151B VAL* 4.8 0.5 + - - +
320B PHE* 3.7 21.8 - - - -
321B VAL 3.8 19.9 + - - +
322B PRO* 3.5 24.2 + - - +
323B ALA* 3.1 3.9 - - - +
324B LEU 2.7 39.3 + - - +
402B THR* 3.0 28.9 + - - +
403B THR 2.7 35.1 + - - -
404B HIS* 3.5 30.5 - - + +
615B GLN* 5.4 5.2 - - - +
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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