Contacts of the strand formed by residues 349 - 357 (chain B) in PDB entry 3F7F
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 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B TYR* 3.5 35.0 - - + -
286B THR* 3.9 33.2 - - + +
336B LEU* 4.2 17.3 - - + -
337B THR 3.6 13.7 - - - +
338B ARG* 4.7 1.1 - - - -
339B PRO* 4.5 3.6 - - - -
348B TYR* 1.3 112.3 - - + +
350B ASN* 1.3 71.9 + - - +
366B LEU 4.5 0.4 - - - -
367B ASN* 3.7 1.6 - - - +
368B VAL* 3.2 35.1 + - + +
373B PHE* 4.3 6.3 - - + -
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Residues in contact with ASN 350 (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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335B VAL 3.7 1.4 - - - +
336B LEU* 3.5 5.5 - - - +
337B THR* 2.8 47.8 + - + +
338B ARG 3.9 8.7 - - - +
339B PRO* 3.8 0.2 - - - -
340B LEU* 3.3 38.6 - - - +
342B LEU* 3.6 7.7 - - - +
347B SER* 3.7 3.6 + - - -
349B LEU* 1.3 91.0 - - - +
351B LEU* 1.3 61.2 + - - +
352B ILE* 4.0 3.3 - - + +
365B ILE* 3.4 26.4 - - + +
366B LEU 3.4 2.2 - - - -
367B ASN* 3.2 20.6 - - - +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.9 20.6 - - + -
298B PHE* 3.6 36.6 - - + -
300B MET* 4.8 3.1 - - + -
334B LEU* 4.3 10.1 - - + -
335B VAL 3.8 3.6 - - - +
336B LEU* 3.7 39.0 - - + +
350B ASN* 1.3 74.0 - - - +
352B ILE* 1.3 61.9 + - - +
353B VAL* 3.6 16.1 + - + +
365B ILE* 3.2 3.5 - - - -
366B LEU* 2.6 64.1 + - + +
368B VAL* 6.3 0.9 - - + -
378B TRP* 5.1 0.2 - - + -
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 3.2 5.4 - - - -
335B VAL* 2.8 48.9 + - + +
337B THR* 4.4 12.8 - - + -
340B LEU* 6.1 3.4 - - + -
350B ASN* 5.2 2.9 - - + +
351B LEU* 1.3 73.7 - - - +
353B VAL* 1.3 62.0 + - - +
363B LEU* 4.0 20.4 - - + -
364B GLN 3.6 5.8 - - - +
365B ILE* 4.2 11.0 - - + +
463B ILE* 3.8 18.9 - - + +
465B LEU* 3.9 21.5 - - + -
471B ILE* 3.3 41.5 - - + -
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.9 13.7 - - + -
331B ILE* 3.3 27.8 - - + -
333B ASP 4.0 1.8 - - - -
334B LEU* 4.5 2.5 - - + +
351B LEU* 3.7 34.3 - - + +
352B ILE* 1.3 78.5 - - - +
354B LEU* 1.3 61.3 + - - +
355B TRP* 3.6 27.6 - - + +
362B LYS 3.6 1.4 - - - +
363B LEU* 3.3 7.3 - - - +
364B GLN* 2.8 41.4 + - + +
378B TRP* 4.1 15.3 - - + -
463B ILE* 4.7 0.9 - - - -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.6 4.6 - - - +
332B VAL* 2.7 60.8 + - + -
333B ASP 3.0 19.3 + - - +
353B VAL* 1.3 73.5 - - - +
355B TRP* 1.3 59.8 + - - +
361B SER* 4.5 7.0 - - - +
362B LYS 3.5 13.7 - - - +
363B LEU* 4.2 20.2 - - + -
460B ALA* 3.9 19.7 - - + -
462B SER* 4.2 6.1 - - - +
463B ILE* 4.0 21.7 - - + +
473B VAL* 4.1 21.5 - - + -
484B TYR* 5.4 1.3 - - - +
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Residues in contact with TRP 355 (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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290B LEU* 4.0 12.3 - - + -
295B ASN* 3.1 35.9 - - - -
298B PHE* 3.7 33.2 - + - -
321B THR* 4.1 10.8 - - + -
323B LEU* 3.7 25.0 - - + +
329B TRP* 3.7 21.5 - - + -
330B SER 3.1 9.0 - - - +
331B ILE* 3.6 34.8 - - + -
332B VAL* 3.6 3.3 - - - +
353B VAL* 3.6 17.1 - - + +
354B LEU* 1.3 76.7 - - - +
356B LYS* 1.3 64.1 + - - +
361B SER* 3.6 5.9 - - - -
362B LYS* 2.8 41.7 + - + +
364B GLN* 2.7 32.1 + - - -
378B TRP* 5.5 1.1 - + - -
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Residues in contact with LYS 356 (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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329B TRP* 3.4 6.2 - - - -
330B SER* 2.8 41.5 + - - +
332B VAL* 3.3 20.8 - - + +
355B TRP* 1.3 76.3 - - - +
357B SER* 1.3 64.7 + - - +
358B GLY 3.0 25.1 - - - +
359B THR* 5.1 0.4 - - - -
360B ALA 3.5 9.6 - - - +
361B SER* 5.0 1.1 - - - -
459B GLU* 2.8 29.1 + - + +
460B ALA* 3.2 29.1 + - + +
476B PHE* 3.3 12.9 - - - -
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Residues in contact with SER 357 (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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328B ILE* 3.2 28.9 + - - +
329B TRP* 3.3 29.3 - - - -
330B SER* 5.4 0.7 - - - -
356B LYS* 1.3 77.5 - - - +
358B GLY* 1.3 61.7 + - - +
359B THR 3.6 0.3 + - - -
360B ALA* 3.0 21.0 + - - +
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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