Contacts of the strand formed by residues 399 - 404 (chain A) in PDB entry 4OI0
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 THR 399 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASP* 4.6 18.9 + - + -
320A VAL 3.2 14.8 - - - +
321A SER* 4.3 9.4 - - - +
322A PHE* 3.6 7.6 - - - -
394A ASP* 2.8 44.8 + - - +
397A LYS* 3.3 27.2 - - + +
398A ARG* 1.3 79.6 - - - +
400A MET* 1.3 63.8 + - - +
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Residues in contact with MET 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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318A PHE 3.8 0.3 - - - +
319A ASP* 3.3 5.1 - - - -
320A VAL* 2.8 53.9 + - + +
322A PHE* 3.6 27.6 - - + -
325A VAL* 4.6 4.3 - - + -
327A LEU* 4.3 9.9 - - + -
362A ILE* 4.2 8.5 - - + -
367A PHE* 6.0 0.2 - - + -
388A CYS* 5.3 0.2 - - - -
390A VAL* 3.9 28.3 - - + -
392A GLU 3.5 13.9 - - - +
393A VAL* 4.6 2.2 - - + -
399A THR* 1.3 74.9 - - - +
401A SER* 1.3 61.4 + - - +
402A ILE* 3.6 18.3 + - + -
414A LEU* 3.5 32.8 - - + -
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Residues in contact with SER 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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317A THR* 4.8 9.9 - - - -
318A PHE 3.4 7.6 - - - -
319A ASP* 2.8 17.7 + - - -
390A VAL* 3.6 2.3 - - - +
391A THR* 2.9 40.0 + - - -
392A GLU* 3.0 30.1 + - - +
400A MET* 1.3 71.6 - - - +
402A ILE* 1.3 64.8 + - - +
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Residues in contact with ILE 402 (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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316A PHE 3.5 1.2 - - - +
317A THR* 3.3 7.0 - - - +
318A PHE* 2.9 67.8 + - + +
320A VAL* 3.9 12.1 - - + -
369A PHE* 4.3 1.1 - - + -
388A CYS* 4.1 31.6 - - + -
389A LEU 3.2 9.2 - - - +
390A VAL* 4.3 4.5 - - + -
391A THR* 4.6 3.6 - - - -
400A MET* 3.6 36.3 - - + +
401A SER* 1.3 79.5 - - - +
403A LEU* 1.3 59.3 + - - +
404A CYS* 4.1 5.6 - - + -
409A ILE* 4.0 13.0 - - + -
414A LEU* 5.6 0.2 - - + -
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Residues in contact with LEU 403 (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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305A PHE* 3.6 34.5 - - + -
306A TYR* 3.7 35.9 - - + +
315A PRO* 3.9 18.2 - - + +
316A PHE 3.4 9.2 - - - +
317A THR* 3.3 21.8 - - - +
388A CYS* 3.2 8.8 - - - +
389A LEU* 2.8 45.8 + - + +
391A THR* 4.4 10.1 - - + +
402A ILE* 1.3 71.4 - - - +
404A CYS* 1.3 58.9 + - - +
423A ASP* 4.1 8.7 - - - +
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Residues in contact with CYS 404 (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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305A PHE* 4.8 0.4 - - - -
315A PRO* 4.3 4.3 - - - -
316A PHE 2.7 36.8 + - - -
318A PHE* 3.8 24.7 - - + -
369A PHE* 3.9 29.2 - - - -
388A CYS* 4.5 0.4 - - + -
402A ILE* 4.1 5.8 - - + -
403A LEU* 1.3 76.8 - - - +
405A PRO* 1.3 75.5 - - - +
406A GLN* 3.2 33.6 + - - +
408A THR 4.6 3.6 - - - -
409A ILE* 4.9 0.2 - - - -
410A PRO* 4.7 0.2 - - - -
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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