Contacts of the strand formed by residues 348 - 353 (chain B) in PDB entry 1SOX
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 GLN 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLN* 3.0 39.6 + - - +
188B ASN 4.7 0.9 - - - +
189B ARG* 2.8 40.9 - - - +
209B ILE* 5.3 0.9 - - + -
346B PRO 4.0 6.3 - - - +
347B VAL* 1.3 76.4 - - - +
349B SER* 1.3 81.7 + - - +
370B TYR* 4.3 15.0 - - + -
371B ALA* 3.3 1.7 - - - +
372B TRP* 2.7 40.2 + - + +
431B ALA* 4.1 2.9 - - - +
439B GLN* 3.7 6.3 - - - +
454B SER 3.0 18.6 - - - +
455B THR* 3.6 16.3 - - + +
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Residues in contact with SER 349 (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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189B ARG* 3.5 20.6 + - - -
348B GLN* 1.3 87.2 + - - +
350B ALA* 1.3 63.1 + - - +
370B TYR* 3.2 18.6 - - - -
371B ALA* 4.0 3.6 - - - +
382B VAL* 5.3 1.1 - - - -
413B TRP* 4.8 1.6 - - - -
429B CYS* 3.3 19.1 + - - -
430B LYS* 3.6 8.1 + - - -
431B ALA* 3.8 12.6 - - - -
439B GLN* 2.6 25.7 + - - -
458B HIS* 4.0 3.5 - - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ARG* 4.6 3.4 - - - -
206B ILE* 4.2 16.8 - - + -
349B SER* 1.3 77.4 + - - +
351B VAL* 1.3 59.9 - - - +
369B GLY* 3.2 4.7 - - - -
370B TYR* 3.1 62.5 + - + +
413B TRP* 3.5 3.1 - - - -
429B CYS* 3.5 9.4 - - - -
458B HIS* 3.7 13.2 - - + +
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Residues in contact with VAL 351 (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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206B ILE* 3.3 8.0 - - - +
350B ALA* 1.3 73.4 - - - +
352B THR* 1.3 61.8 + - - +
353B GLN 3.4 26.0 - - - +
354B PRO* 4.0 9.2 - - + +
355B ARG* 4.5 3.1 + - - -
367B VAL* 3.8 11.0 - - + -
368B LYS 3.7 6.3 - - - +
413B TRP* 4.1 4.5 - - + -
427B ILE* 4.1 21.8 - - + +
429B CYS* 3.7 28.0 - - + +
458B HIS* 2.8 35.4 + - - +
460B VAL* 3.9 14.9 - - + +
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Residues in contact with THR 352 (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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121B ALA 3.4 20.2 - - - +
122B GLU* 3.9 16.6 + - - -
124B LEU* 3.8 18.6 - - + -
125B ALA* 3.6 16.4 + - + +
126B GLU* 5.3 1.9 + - - -
206B ILE* 4.0 14.6 - - + -
351B VAL* 1.3 74.6 - - - +
353B GLN* 1.3 64.1 + - - +
354B PRO 4.0 3.6 - - - -
355B ARG* 3.9 21.3 + - - +
368B LYS* 2.8 18.0 + - - +
369B GLY* 3.5 9.6 - - - -
370B TYR* 4.0 20.9 - - + -
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Residues in contact with GLN 353 (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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46B LYS* 5.6 5.9 - - - +
122B GLU* 4.9 8.1 + - - +
126B GLU* 4.0 15.3 + - - +
351B VAL* 3.4 1.9 - - - +
352B THR* 1.3 84.2 - - - +
354B PRO* 1.3 70.1 - - + +
365B LEU* 5.8 1.1 - - + -
366B THR* 3.4 23.2 - - - +
367B VAL* 3.3 6.6 - - - +
368B LYS* 2.9 58.9 + - + +
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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