Contacts of the strand formed by residues 348 - 352 (chain B) in PDB entry 4WQ6
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 LEU 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B TRP* 6.3 0.2 - - + -
299B ILE* 4.4 7.0 - - + -
307B PRO* 4.0 0.2 - - - +
308B LEU* 3.4 26.7 - - + +
310B ILE* 3.8 27.4 - - + -
328B LEU* 4.2 19.1 - - + -
332B PHE* 3.5 45.5 - - + -
344B LEU* 3.5 18.9 - - + +
345B PRO* 3.1 8.9 + - + +
346B PRO 3.2 1.8 + - - -
347B TYR* 1.3 91.8 - - + +
349B ARG* 1.3 90.0 + - - +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PRO* 4.7 13.7 - - + -
308B LEU 2.9 7.6 + - - +
309B ILE* 3.3 20.3 - - + -
310B ILE* 2.8 25.6 + - - +
343B LEU* 4.0 21.9 - - - +
344B LEU* 3.2 21.0 + - - +
345B PRO 3.0 15.9 + - - -
346B PRO* 4.0 17.4 + - - +
348B LEU* 1.3 93.4 + - - +
350B VAL* 1.3 69.8 + - - +
376B GLU* 3.3 23.4 + - - +
377B ASN* 3.5 19.3 + - - +
378B ILE 6.2 0.2 - - - -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ILE* 3.7 5.5 - - - +
310B ILE* 3.3 14.8 - - + +
312B PRO* 3.9 19.7 - - + -
321B VAL* 5.4 5.8 - - + -
324B VAL* 4.2 12.3 - - + -
325B LEU* 4.2 19.5 - - + -
328B LEU* 3.9 26.2 - - + -
344B LEU* 4.4 3.1 - - + -
349B ARG* 1.3 83.6 - - - +
351B ILE* 1.3 67.4 + - - +
352B GLN 4.6 1.6 - - - +
377B ASN 3.1 9.7 + - - +
378B ILE* 3.3 17.9 - - + -
379B ALA* 3.0 23.2 + - - +
601B 3TQ 4.8 0.3 + - - -
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B HIS* 4.8 0.9 - - + -
193B PHE* 3.6 28.9 - - + -
275B SER* 3.8 7.6 - - - +
309B ILE* 3.5 16.6 - - + +
310B ILE 3.0 4.0 + - - -
311B ARG* 3.5 30.2 - - + +
312B PRO* 3.2 19.6 - - - +
350B VAL* 1.3 78.6 - - - +
352B GLN* 1.3 64.8 + - - +
353B GLY* 4.4 1.6 - - - +
379B ALA 3.2 12.6 - - - +
380B PHE 4.1 5.6 - - - +
381B GLY 3.9 14.4 - - - +
601B 3TQ 3.6 38.1 - - + +
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO* 3.6 25.8 + - + +
313B ASP* 5.1 1.6 - - - +
314B SER 5.4 2.2 + - - +
315B GLY 5.6 0.6 + - - -
317B PRO* 4.1 16.6 - - - +
320B THR* 5.2 2.6 - - - +
321B VAL* 3.6 28.6 + - + +
350B VAL* 5.6 0.2 - - + -
351B ILE* 1.3 71.0 - - - +
353B GLY* 1.3 58.9 + - - +
354B ASP* 2.8 42.2 + - - +
356B VAL* 3.6 18.1 - - + +
364B ILE* 4.1 12.8 - - + -
378B ILE* 4.3 5.9 - - + +
379B ALA 3.0 6.5 + - - -
380B PHE* 3.3 16.9 - - + -
381B GLY 2.9 18.9 + - - -
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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
------------------------------------------------------------
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