Contacts of the strand formed by residues 360 - 368 (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 ALA 360 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B TRP* 4.2 14.1 - - + -
356B LYS* 3.5 5.4 - - - +
357B SER* 3.0 35.9 + - - +
358B GLY 3.2 0.6 - - - -
359B THR* 1.3 81.8 + - - +
361B SER* 1.3 60.6 + - - +
384B LYS* 6.6 0.7 - - - +
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Residues in contact with SER 361 (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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6B ARG* 4.2 13.1 + - - +
329B TRP* 4.0 7.3 - - - -
354B LEU* 4.5 5.5 - - - +
355B TRP 3.6 10.8 - - - -
356B LYS* 5.0 0.7 - - - -
359B THR 4.1 2.1 + - - -
360B ALA* 1.3 75.8 - - - +
362B LYS* 1.3 65.1 + - - +
383B ASN* 3.3 22.8 + - - +
458B ASN 6.1 0.4 - - - -
460B ALA* 4.1 25.5 - - - +
484B TYR* 3.6 18.9 + - - -
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Residues in contact with LYS 362 (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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322B ASN 5.5 1.7 + - - -
323B LEU* 3.9 23.3 - - + -
329B TRP* 3.8 38.6 - - + +
353B VAL 3.6 1.0 - - - +
354B LEU* 3.5 4.8 - - - +
355B TRP* 2.8 49.7 + - + +
361B SER* 1.3 78.2 - - - +
363B LEU* 1.3 62.3 + - - +
364B GLN* 4.2 6.4 - - + +
380B GLU* 2.7 32.7 + - - -
383B ASN* 3.5 16.4 - - - +
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Residues in contact with LEU 363 (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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4B LEU* 4.3 14.6 - - + -
352B ILE* 4.0 12.6 - - + -
353B VAL 3.3 6.5 - - - +
354B LEU* 4.2 20.6 - - + -
362B LYS* 1.3 75.0 - - - +
364B GLN* 1.3 77.6 + - - +
365B ILE* 4.8 1.6 - - + -
381B SER* 3.0 42.0 + - - +
383B ASN* 3.1 8.4 + - - +
463B ILE* 5.1 1.8 - - + -
471B ILE* 3.7 28.3 - - + -
473B VAL* 4.4 10.5 - - + -
484B TYR* 3.9 34.3 - - + -
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Residues in contact with GLN 364 (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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321B THR* 6.0 0.5 - - - -
322B ASN* 3.5 29.4 + - - +
323B LEU* 4.2 5.6 - - - +
352B ILE* 3.6 0.7 - - - -
353B VAL* 2.8 32.3 + - + +
355B TRP* 2.7 37.3 + - + +
362B LYS* 4.2 8.6 - - + +
363B LEU* 1.3 85.5 - - - +
365B ILE* 1.3 70.3 + - - +
366B LEU 4.3 0.2 - - - -
378B TRP* 3.8 23.6 - - + -
379B ILE 3.4 12.3 - - - +
380B GLU* 3.0 35.3 + - - +
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Residues in contact with ILE 365 (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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4B LEU* 3.9 22.0 - - + -
340B LEU* 3.8 20.4 - - + -
342B LEU* 4.1 12.1 - - + -
350B ASN* 3.4 33.7 - - + +
351B LEU 3.2 8.7 - - - +
352B ILE* 4.2 8.1 - - + -
363B LEU* 4.8 2.7 - - + -
364B GLN* 1.3 80.3 - - - +
366B LEU* 1.3 62.0 + - - +
367B ASN 3.6 1.4 + - - -
378B TRP* 3.7 3.8 - - - -
379B ILE* 2.9 41.0 + - + +
471B ILE* 3.5 32.3 - - + -
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Residues in contact with LEU 366 (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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298B PHE* 5.1 1.6 - - + -
300B MET* 3.9 16.6 - - + -
319B ILE* 3.8 31.2 - - + -
349B LEU 4.5 0.2 - - - -
350B ASN* 3.4 5.2 - - - -
351B LEU* 2.6 56.3 + - + +
365B ILE* 1.3 70.8 - - - +
367B ASN* 1.3 62.4 + - - +
368B VAL* 3.9 14.0 + - + +
376B TYR* 3.8 21.5 - - + -
377B GLU 4.1 2.0 - - - +
378B TRP* 3.3 51.8 - - + +
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Residues in contact with ASN 367 (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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342B LEU* 4.1 20.8 - - + +
344B VAL* 4.5 16.7 + - - +
346B ALA 3.4 19.7 + - - -
347B SER* 2.8 32.3 + - - -
350B ASN* 3.2 13.1 - - - +
365B ILE 3.6 0.8 + - - +
366B LEU* 1.3 70.7 - - - +
368B VAL* 1.3 62.8 + - - +
369B ASN* 4.4 7.1 + - - +
376B TYR* 3.2 4.5 - - - +
377B GLU* 2.8 51.1 + - + +
379B ILE* 4.8 5.8 - - + +
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Residues in contact with VAL 368 (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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300B MET* 4.4 23.1 - - - -
319B ILE* 4.5 2.9 - - + -
336B LEU* 6.5 0.9 - - + -
347B SER* 3.6 0.9 - - - -
348B TYR* 2.8 42.7 + - + -
349B LEU* 3.2 43.4 + - + +
351B LEU* 6.3 1.1 - - + -
366B LEU* 4.4 14.6 - - + +
367B ASN* 1.3 73.8 + - - +
369B ASN* 1.3 54.8 + - - +
370B ASP 3.9 5.2 - - - +
373B PHE* 4.7 13.9 - - + -
375B ASN 3.8 7.0 - - - +
376B TYR* 4.0 11.0 - - + -
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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