Contacts of the strand formed by residues 393 - 401 (chain A) in PDB entry 5OAQ
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 PHE 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A VAL* 3.4 26.5 - - + -
335A CYS 3.6 8.1 - - - -
336A SER* 5.7 1.8 - - - -
369A TYR* 4.2 7.4 - + - -
370A MET* 3.3 35.4 - - + -
373A PHE* 3.5 41.1 - + + -
389A VAL 4.2 1.6 - - - +
390A LEU* 3.2 31.6 + - + +
391A GLU 3.5 0.4 - - - -
392A ASN* 1.3 79.3 - - - +
394A THR* 1.3 70.0 + - - +
395A ILE* 3.9 12.6 - - + -
414A VAL* 4.9 0.5 - - - +
415A PHE* 3.9 39.3 + + - -
502A MYR 4.8 4.0 - - + -
68L LEU* 5.5 2.0 - - + -
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Residues in contact with THR 394 (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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273A LYS* 2.8 43.0 + - + -
274A PHE* 3.3 28.2 - - + -
334A VAL* 3.7 2.6 - - - +
335A CYS* 2.8 44.6 + - - +
391A GLU 5.2 2.0 - - - +
392A ASN 5.2 0.7 - - - -
393A PHE* 1.3 86.3 - - - +
395A ILE* 1.3 67.0 + - - +
413A TYR 3.4 11.2 - - - +
414A VAL* 4.2 12.3 - - + -
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Residues in contact with ILE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 6.2 0.2 - - + -
274A PHE* 3.6 6.0 - - - -
332A THR* 3.5 30.3 - - + -
333A LYS 3.3 8.1 - - - +
334A VAL* 4.4 7.2 - - + -
370A MET* 4.7 2.0 - - - -
393A PHE* 3.9 22.7 - - + -
394A THR* 1.3 81.1 - - - +
396A LEU* 1.3 64.0 + - - +
397A GLN 4.1 0.2 - - - -
413A TYR* 2.7 59.9 + - + -
415A PHE* 4.0 10.3 - - + -
502A MYR 3.7 46.7 - - + -
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Residues in contact with LEU 396 (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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274A PHE* 3.9 15.2 - - + -
275A PRO* 4.3 21.1 - - + -
280A GLY* 5.4 0.9 - - - -
281A LEU* 4.2 22.9 - - + +
284A LEU* 4.7 8.5 - - + -
331A SER 3.5 2.1 - - - +
332A THR* 3.4 1.4 - - - -
333A LYS* 2.8 55.0 + - + +
335A CYS* 4.9 2.9 - - - -
395A ILE* 1.3 75.7 - - - +
397A GLN* 1.3 57.3 + - - +
398A VAL* 4.1 18.8 + - + +
410A CYS* 3.8 20.2 - - - -
411A ILE 3.6 14.6 - - - +
412A ALA* 4.0 17.3 - - + -
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Residues in contact with GLN 397 (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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226A MET* 4.0 4.9 - - - -
229A PHE* 3.6 15.1 - - - -
320A TYR* 2.7 33.7 + - - -
330A CYS* 3.7 24.5 - - - -
331A SER 3.3 3.1 - - - -
332A THR* 4.0 13.0 - - + +
395A ILE 4.1 0.2 - - - -
396A LEU* 1.3 73.4 - - - +
398A VAL* 1.3 62.6 + - - +
399A VAL* 3.7 12.8 - - + +
409A LEU 3.8 1.0 - - - +
410A CYS* 3.3 3.8 - - - -
411A ILE* 2.7 49.2 + - + +
413A TYR* 2.7 43.4 + - + -
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Residues in contact with VAL 398 (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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284A LEU* 3.6 41.7 - - + -
329A THR 3.5 3.1 - - - +
331A SER* 2.8 49.7 + - - +
333A LYS* 6.2 2.9 - - + -
396A LEU* 4.1 14.1 - - + +
397A GLN* 1.3 77.0 - - - +
399A VAL* 1.3 62.8 - - - +
400A THR* 3.6 19.1 + - - +
407A THR* 4.5 9.9 - - + +
409A LEU 3.6 6.3 - - - +
410A CYS* 4.0 11.4 - - - -
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Residues in contact with VAL 399 (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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224A LEU* 3.5 27.6 - - + -
320A TYR* 4.4 11.7 - - + +
328A ILE* 4.0 21.5 - - + -
329A THR 3.2 9.6 - - - +
330A CYS* 4.0 13.0 - - + -
397A GLN* 3.7 27.4 - - + +
398A VAL* 1.3 75.4 - - - +
400A THR* 1.3 62.7 + - - +
407A THR* 3.8 2.6 - - - +
408A LEU* 2.9 25.2 + - + +
409A LEU* 2.8 28.8 + - + +
411A ILE* 5.4 0.7 - - + -
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Residues in contact with THR 400 (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 6.6 - - - +
329A THR* 2.8 42.4 + - - +
398A VAL* 3.6 20.3 + - - +
399A VAL* 1.3 76.1 - - - +
401A ASN* 1.3 76.0 + - - +
405A GLN* 3.4 40.2 - - - +
406A GLU 3.3 10.7 + - - +
407A THR* 4.8 2.8 + - - -
408A LEU* 3.6 5.4 - - - -
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Residues in contact with ASN 401 (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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324A GLU* 5.4 2.8 + - - -
326A MET* 3.9 27.0 - - - +
327A ILE 3.8 8.8 + - - +
328A ILE* 4.9 0.2 - - - -
400A THR* 1.3 70.1 - - - +
402A ARG* 1.3 56.6 + - - +
403A ASP* 3.0 21.1 + - - +
404A THR* 3.1 35.1 + - - +
405A GLN* 2.7 34.0 + - - -
406A GLU* 3.0 16.0 + - + +
408A LEU* 3.5 20.5 - - + +
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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