Contacts of the strand formed by residues 339 - 343 (chain B) in PDB entry 6S1M
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 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B ALA* 5.1 9.4 - - + -
188B PRO 5.9 1.8 - - - +
190B LEU* 5.5 1.8 - - + -
335B THR* 4.5 0.2 - - - -
336B ILE 2.9 32.5 + - - +
337B ASP 3.3 6.3 - - - +
338B GLY* 1.3 75.5 - - - +
340B ARG* 1.3 61.1 + - - +
341B PHE* 3.5 25.7 - - + -
400B HIS* 4.2 13.9 - - + -
401B VAL* 3.7 22.4 - - + -
442B LEU* 4.2 31.6 - - + +
445B LEU* 5.0 15.0 - - + -
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Residues in contact with ARG 340 (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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185B LYS* 4.1 19.8 - - - +
334B ALA 3.3 12.1 - - - +
335B THR* 4.2 23.7 + - + +
338B GLY 3.5 4.4 + - - -
339B VAL* 1.3 74.3 - - - +
341B PHE* 1.3 62.0 + - - +
397B GLU* 2.9 40.2 + - - -
398B CYS 4.3 12.1 - - - -
399B PRO* 4.3 5.7 - - + +
400B HIS* 3.3 37.0 + - - +
401B VAL 3.3 23.9 + - - +
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Residues in contact with PHE 341 (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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196B VAL* 4.6 18.6 - - + -
198B LEU* 5.3 8.1 - - + -
242B ILE* 5.1 6.3 - - + -
332B TYR* 4.4 2.9 - - + -
333B GLN* 3.3 5.6 - - - +
334B ALA* 2.9 35.1 + - + +
336B ILE* 3.7 37.2 - - + -
339B VAL* 3.5 38.8 - - + -
340B ARG* 1.3 76.3 - - - +
342B LEU* 1.3 61.6 + - - +
399B PRO* 5.0 1.8 - - - -
401B VAL* 3.9 29.2 - - + -
403B PHE* 4.5 20.0 - + + -
440B VAL* 4.8 9.0 - - + -
442B LEU* 4.4 18.4 - - + -
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Residues in contact with LEU 342 (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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39B PHE* 5.8 2.7 - - + -
331B PRO* 5.6 4.7 - - + -
332B TYR 3.2 9.4 - - - +
333B GLN* 3.4 37.9 - - + +
341B PHE* 1.3 74.8 - - - +
343B GLY* 1.3 68.8 + - - +
344B THR* 5.5 1.8 - - + -
374B ILE* 4.3 25.1 - - + -
395B PHE* 4.5 18.4 - - + -
399B PRO* 4.4 18.4 - - + -
401B VAL 3.5 5.9 + - - -
402B TYR* 3.5 28.7 - - + -
403B PHE* 3.3 25.8 + - - -
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Residues in contact with GLY 343 (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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295B MET* 4.5 2.0 - - - -
330B ASN 3.4 2.6 - - - +
331B PRO* 3.6 4.3 - - - +
332B TYR* 2.9 34.0 + - - +
342B LEU* 1.3 82.0 - - - +
344B THR* 1.3 65.7 + - - +
402B TYR* 5.3 1.6 - - - -
403B PHE* 3.6 31.1 - - - -
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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