Contacts of the strand formed by residues 349 - 357 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR* 3.5 34.8 - - + -
286A THR* 3.9 33.0 - - + +
336A LEU* 4.3 17.0 - - + -
337A THR 3.6 13.7 - - - +
338A ARG* 4.7 1.1 - - - -
339A PRO* 4.5 3.6 - - + -
348A TYR* 1.3 112.8 - - + +
350A ASN* 1.3 71.8 + - - +
366A LEU 4.5 0.2 - - - -
367A ASN* 3.7 1.6 - - - +
368A VAL* 3.2 35.3 + - + +
373A PHE* 4.3 6.1 - - + -
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A VAL 3.7 1.6 - - - +
336A LEU* 3.5 5.5 - - - +
337A THR* 2.8 47.5 + - + +
338A ARG 3.8 9.0 - - - +
339A PRO* 3.8 0.2 - - - -
340A LEU* 3.3 39.2 - - - +
342A LEU* 3.6 7.5 - - - +
347A SER* 3.7 3.6 + - - -
349A LEU* 1.3 90.8 - - - +
351A LEU* 1.3 61.1 + - - +
352A ILE* 4.0 3.3 - - + +
365A ILE* 3.4 26.4 - - + +
366A LEU 3.3 2.0 - - - -
367A ASN* 3.2 20.8 - - - +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A VAL* 3.9 22.7 - - + -
298A PHE* 3.6 36.8 - - + -
300A MET* 4.7 0.9 - - + -
334A LEU* 4.3 10.1 - - + -
335A VAL 3.8 3.6 - - - +
336A LEU* 3.7 39.3 - - + +
350A ASN* 1.3 72.7 - - - +
352A ILE* 1.3 62.4 + - - +
353A VAL* 3.6 15.3 + - + +
365A ILE* 3.1 3.9 - - - -
366A LEU* 2.6 62.6 + - + +
368A VAL* 6.3 0.9 - - + -
378A TRP* 5.1 0.2 - - + -
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Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU* 3.2 5.7 - - - -
335A VAL* 2.9 48.8 + - + +
337A THR* 4.4 12.8 - - + -
340A LEU* 6.1 3.4 - - + -
350A ASN* 5.2 2.9 - - + +
351A LEU* 1.3 73.3 - - - +
353A VAL* 1.3 62.2 + - - +
363A LEU* 4.0 21.1 - - + -
364A GLN 3.6 5.4 - - - +
365A ILE* 4.2 10.8 - - + +
463A ILE* 3.8 18.9 - - + +
465A LEU* 3.8 21.8 - - + -
469A GLU 5.5 0.4 - - - +
471A ILE* 3.3 41.5 - - + -
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Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A PHE* 3.9 13.5 - - + -
331A ILE* 3.3 27.6 - - + -
333A ASP 4.0 1.8 - - - -
334A LEU* 4.5 2.5 - - + +
351A LEU* 3.7 34.3 - - + +
352A ILE* 1.3 78.8 - - - +
354A LEU* 1.3 62.0 + - - +
355A TRP* 3.6 27.6 - - + +
362A LYS 3.6 1.2 - - - +
363A LEU* 3.3 7.1 - - - +
364A GLN* 2.8 42.1 + - + +
378A TRP* 4.1 15.7 - - + -
463A ILE* 4.7 0.9 - - - -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ILE* 3.6 4.2 - - - +
332A VAL* 2.7 61.2 + - + -
333A ASP 3.0 18.5 + - - +
353A VAL* 1.3 73.9 - - - +
355A TRP* 1.3 59.4 + - - +
361A SER* 4.5 6.7 - - - +
362A LYS 3.5 13.7 - - - +
363A LEU* 4.2 20.6 - - + -
460A ALA* 3.9 20.2 - - + -
462A SER* 4.2 5.8 - - - +
463A ILE* 3.9 21.7 - - + +
473A VAL* 4.0 21.1 - - + -
484A TYR* 5.4 2.0 - - + +
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Residues in contact with TRP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 4.0 11.9 - - + -
295A ASN* 3.1 35.7 - - - -
298A PHE* 3.7 33.0 - + - -
321A THR* 4.1 11.0 - - + -
323A LEU* 3.7 25.3 - - + +
329A TRP* 3.7 22.4 - - + -
330A SER 3.1 8.5 - - - -
331A ILE* 3.5 35.4 - - + -
332A VAL* 3.6 3.3 - - - +
353A VAL* 3.6 18.2 - - + +
354A LEU* 1.3 76.3 - - - +
356A LYS* 1.3 63.5 + - - +
361A SER* 3.6 5.9 - - - -
362A LYS* 2.8 42.2 + - + +
364A GLN* 2.6 32.3 + - - -
378A TRP* 5.5 1.1 - + - -
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A TRP* 3.4 6.6 - - - -
330A SER* 2.8 41.5 + - - +
332A VAL* 3.3 20.6 - - + +
355A TRP* 1.3 76.3 - - - +
357A SER* 1.3 65.6 + - - +
358A GLY 3.0 25.6 - - - +
359A THR* 5.1 0.4 - - - -
360A ALA 3.5 9.9 - - - +
361A SER* 5.0 1.1 - - - -
459A GLU* 2.8 29.9 + - + +
460A ALA* 3.2 29.2 + - + +
476A PHE* 3.3 13.3 - - - -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ILE* 3.2 29.3 + - - +
329A TRP* 3.4 28.7 - - - -
330A SER* 5.4 0.4 - - - -
356A LYS* 1.3 77.8 - - - +
358A GLY* 1.3 61.6 + - - +
359A THR 3.6 0.3 + - - -
360A ALA* 3.0 21.7 + - - +
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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