Contacts of the strand formed by residues 360 - 368 (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 ALA 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A TRP* 4.2 14.4 - - + -
356A LYS* 3.5 5.4 - - - +
357A SER* 3.0 35.7 + - - +
358A GLY 3.2 0.4 - - - -
359A THR* 1.3 82.0 + - - +
361A SER* 1.3 60.5 + - - +
384A LYS* 6.6 0.9 - - - +
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Residues in contact with SER 361 (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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6A ARG* 4.2 13.4 + - - +
329A TRP* 4.0 7.3 - - - -
354A LEU* 4.5 4.9 - - - -
355A TRP 3.6 10.8 - - - -
356A LYS* 5.0 0.4 - - - -
359A THR 4.1 2.1 + - - -
360A ALA* 1.3 75.5 - - - +
362A LYS* 1.3 64.7 + - - +
383A ASN* 3.3 22.8 + - - +
458A ASN 6.1 0.7 - - - -
460A ALA* 4.1 25.2 - - - +
484A TYR* 3.6 19.8 + - - -
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Residues in contact with LYS 362 (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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322A ASN 5.5 1.7 + - - -
323A LEU* 3.9 23.1 - - + -
329A TRP* 3.8 38.4 - - + +
353A VAL 3.6 1.2 - - - +
354A LEU* 3.5 5.0 - - - +
355A TRP* 2.8 50.5 + - + +
361A SER* 1.3 77.5 - - - +
363A LEU* 1.3 62.3 + - - +
364A GLN* 4.2 6.9 - - + +
380A GLU* 2.7 32.7 + - - -
383A ASN* 3.5 16.4 - - - +
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Residues in contact with LEU 363 (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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4A LEU* 4.3 14.6 - - + -
352A ILE* 4.0 12.1 - - + -
353A VAL 3.3 6.5 - - - +
354A LEU* 4.2 21.1 - - + -
362A LYS* 1.3 75.7 - - - +
364A GLN* 1.3 75.5 + - - +
365A ILE* 4.9 1.6 - - + -
380A GLU* 4.3 0.2 - - - -
381A SER* 3.0 41.7 + - - +
383A ASN* 3.1 8.8 + - - +
463A ILE* 5.1 1.8 - - + -
471A ILE* 3.7 29.2 - - + -
473A VAL* 4.4 4.3 - - + -
484A TYR* 3.8 40.8 - - + -
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Residues in contact with GLN 364 (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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321A THR* 6.0 0.5 - - - -
322A ASN* 3.5 29.4 + - - +
323A LEU* 4.2 5.3 - - - +
351A LEU 4.4 0.2 - - - -
352A ILE* 3.6 0.7 - - - -
353A VAL* 2.8 32.3 + - + +
355A TRP* 2.6 37.1 + - + +
362A LYS* 4.2 8.6 - - + +
363A LEU* 1.3 84.9 - - - +
365A ILE* 1.3 70.0 + - - +
366A LEU 4.3 0.4 - - - -
378A TRP* 3.8 23.7 - - + -
379A ILE 3.4 12.3 - - - +
380A GLU* 3.0 35.4 + - - +
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Residues in contact with ILE 365 (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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4A LEU* 3.9 22.0 - - + -
340A LEU* 3.8 20.6 - - + -
342A LEU* 4.1 11.7 - - + -
350A ASN* 3.4 33.4 - - + +
351A LEU 3.1 9.0 - - - +
352A ILE* 4.2 7.6 - - + -
363A LEU* 4.9 2.9 - - + -
364A GLN* 1.3 80.7 - - - +
366A LEU* 1.3 62.6 + - - +
367A ASN 3.6 1.6 + - - -
378A TRP* 3.7 3.6 - - - -
379A ILE* 3.0 40.2 + - + +
471A ILE* 3.5 32.1 - - + -
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Residues in contact with LEU 366 (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* 5.1 1.6 - - + -
300A MET* 3.9 16.6 - - + -
319A ILE* 3.8 31.0 - - + -
349A LEU 4.5 0.2 - - - -
350A ASN* 3.3 5.4 - - - -
351A LEU* 2.6 55.3 + - + +
365A ILE* 1.3 71.4 - - - +
367A ASN* 1.3 62.4 + - - +
368A VAL* 3.9 13.8 + - + +
376A TYR* 3.8 21.5 - - + -
377A GLU 4.0 2.0 - - - +
378A TRP* 3.3 52.5 - - + +
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Residues in contact with ASN 367 (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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342A LEU* 4.1 21.3 - - + +
344A VAL* 4.5 16.9 + - - +
346A ALA 3.4 19.3 + - - -
347A SER* 2.8 32.1 + - - -
350A ASN* 3.2 12.9 - - - +
365A ILE 3.6 0.8 + - - +
366A LEU* 1.3 71.4 - - - +
368A VAL* 1.3 62.2 + - - +
369A ASN* 4.4 7.3 + - - +
376A TYR* 3.2 4.5 - - - +
377A GLU* 2.8 51.6 + - + +
379A ILE* 4.8 6.0 - - + +
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Residues in contact with VAL 368 (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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300A MET* 4.4 23.3 - - - -
319A ILE* 4.5 3.1 - - + -
336A LEU* 6.5 0.4 - - + -
347A SER* 3.6 0.9 - - - -
348A TYR* 2.8 42.4 + - + -
349A LEU* 3.2 43.4 + - + +
351A LEU* 6.3 1.1 - - + -
366A LEU* 4.4 14.6 - - + +
367A ASN* 1.3 73.8 + - - +
369A ASN* 1.3 55.4 + - - +
370A ASP 4.6 4.9 - - - +
373A PHE* 4.6 13.2 - - + -
375A ASN 3.8 7.0 - - - +
376A 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