Contacts of the strand formed by residues 385 - 392 (chain A) in PDB entry 4Y5U
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 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A MET* 3.5 5.8 - - - +
316A VAL* 3.0 30.4 + - + +
384A CYS* 1.3 77.4 - - - +
386A VAL* 1.3 64.7 + - - +
406A LEU* 3.9 16.6 - - + -
407A SER* 3.5 27.8 - - - +
408A LEU 3.9 2.5 - - - +
410A LEU* 3.9 6.5 - - - -
440A PHE* 3.8 17.9 - - + -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.3 12.3 - - + -
289A PHE* 4.9 8.7 - - + -
313A ALA* 4.2 4.0 - - + -
314A ASP 3.2 25.1 - - - +
315A MET* 3.9 12.1 - - - -
340A ILE* 4.2 11.4 - - + -
363A LEU* 5.4 3.1 - - + -
385A ALA* 1.3 73.9 - - - +
387A LEU* 1.3 60.0 + - - +
388A PHE* 3.5 37.1 - - + -
406A LEU* 3.6 2.2 - - - -
407A SER* 2.7 37.2 + - - +
410A LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 387 (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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312A ARG 3.5 2.1 - - - +
313A ALA* 3.6 1.0 - - - -
314A ASP* 2.8 39.7 + - + +
316A VAL* 3.8 30.3 - - + -
323A GLU* 6.0 3.8 - - - +
385A ALA 3.9 2.0 + - - -
386A VAL* 1.3 72.3 - - - +
388A PHE* 1.3 68.7 + - - +
389A SER* 4.0 10.7 + - - +
404A GLN* 4.2 31.9 - - + +
405A ALA 3.3 19.1 - - - +
406A LEU* 3.8 19.1 - - + -
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Residues in contact with PHE 388 (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 PHE* 3.9 4.8 - - + -
275A VAL* 4.0 22.7 - - + -
279A PRO* 5.1 0.9 - - + -
291A ALA* 3.7 24.5 - - + -
293A VAL* 3.5 30.5 - - + -
311A VAL* 4.3 6.1 - - + -
312A ARG 3.1 8.7 - - - +
313A ALA* 4.2 7.6 - - + -
360A PHE* 3.8 38.4 - + - -
363A LEU* 4.9 1.8 - - + -
386A VAL* 3.5 40.6 - - + -
387A LEU* 1.3 74.9 - - - +
389A SER* 1.3 60.6 + - - +
403A LEU 3.7 0.2 - - - +
404A GLN* 3.3 5.5 - - - +
405A ALA* 2.6 43.1 + - + +
407A SER* 4.4 2.9 - - - -
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Residues in contact with SER 389 (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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310A LEU 3.9 1.2 - - - +
311A VAL* 3.4 4.6 - - - +
312A ARG* 2.8 47.6 + - - +
314A ASP* 5.3 3.8 - - - -
387A LEU* 4.4 11.1 - - - +
388A PHE* 1.3 76.1 + - - +
390A ALA* 1.3 60.7 + - - +
403A LEU 3.3 3.0 + - - -
404A GLN* 3.7 22.9 + - - +
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Residues in contact with ALA 390 (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 PHE* 4.1 15.0 - - + -
309A PRO* 4.8 9.2 - - + -
310A LEU 4.0 9.2 - - - +
311A VAL* 4.0 22.7 - - + -
347A LEU* 5.1 2.7 - - + -
389A SER* 1.3 76.1 - - - +
391A SER* 1.3 60.0 + - - +
392A PHE* 6.3 0.4 - - + -
402A GLN* 3.5 4.2 - - - +
403A LEU* 2.6 41.8 + - + +
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Residues in contact with SER 391 (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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309A PRO* 4.2 12.3 - - - +
310A LEU 4.7 3.0 + - - -
390A ALA* 1.3 77.5 - - - +
392A PHE* 1.3 62.6 + - - +
400A PRO* 5.2 5.0 - - - +
401A ILE 3.1 15.5 - - - -
402A GLN* 3.5 24.2 + - - -
403A LEU 4.4 0.2 - - - +
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Residues in contact with PHE 392 (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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269A VAL* 3.8 26.2 - - + -
295A PHE* 4.0 13.2 - + - -
301A PHE* 4.4 2.7 - - + -
302A LEU* 3.8 23.3 - - + -
309A PRO* 3.9 22.4 - - + -
347A LEU* 6.4 0.4 - - + -
390A ALA* 6.4 0.2 - - + -
391A SER* 1.3 76.2 - - - +
393A THR* 1.3 64.9 + - - +
394A LEU* 3.5 50.0 - - + -
400A PRO* 4.2 2.9 - - - -
401A ILE* 2.5 47.4 + - + +
403A LEU* 3.9 26.5 - - + -
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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