Contacts of the strand formed by residues 386 - 391 (chain B) in PDB entry 1T4O
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 HIS 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A TYR* 2.7 34.3 + + - -
379A GLY 4.0 3.2 + - - -
381A ALA* 3.6 27.8 - - + -
384B ARG* 2.7 33.6 + - + +
385B LEU* 1.3 77.0 - - - +
387B TYR* 1.3 66.5 + - - +
388B VAL* 3.6 24.3 - - + +
404B CYS* 3.6 3.5 - - - -
405B ARG* 2.7 44.5 + - + +
406B VAL 3.4 25.1 - - - -
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Residues in contact with TYR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 4.2 10.4 - - - +
371B LYS* 3.5 45.1 - - + +
374B LEU* 3.8 12.5 - - - +
385B LEU* 4.3 14.0 - - + +
386B HIS* 1.3 81.7 - - - +
388B VAL* 1.3 64.0 + - - +
402B VAL* 4.1 14.4 - - + -
403B GLU 3.3 7.2 - - - +
404B CYS* 3.6 33.7 - - + -
424B GLY* 3.5 26.2 - - - -
427B ALA* 4.6 0.2 - - + -
428B ALA* 3.3 21.0 - - + +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TYR* 3.7 1.8 - - - +
381A ALA* 4.2 18.8 - - - +
384A ARG* 4.2 15.9 - - - -
386B HIS* 3.6 24.0 - - + -
387B TYR* 1.3 76.2 - - - +
389B THR* 1.3 71.1 + - - +
390B VAL* 3.4 2.5 + - + -
402B VAL* 3.4 4.3 - - - -
403B GLU* 2.9 31.6 + - - +
405B ARG* 3.5 50.9 - - + +
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Residues in contact with THR 389 (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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384A ARG* 3.4 34.9 + - - +
386A HIS* 6.0 0.2 - - - -
388B VAL* 1.3 75.3 - - - +
390B VAL* 1.3 59.4 + - - +
391B LYS 3.4 31.9 - - - +
392B LYS* 3.7 19.7 - - + +
400B SER* 5.1 0.2 - - - +
401B ILE 3.5 7.0 - - - +
402B VAL* 3.9 13.9 - - + +
420B ILE* 3.9 23.8 - - + +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 5.1 4.0 - - - +
386A HIS* 4.3 28.5 - - + -
388B VAL* 3.4 6.3 + - + -
389B THR* 1.3 73.9 - - - +
391B LYS* 1.3 62.1 + - + +
401B ILE* 2.9 40.7 + - + +
402B VAL 4.4 0.9 - - - +
403B GLU* 3.6 29.4 - - + +
405B ARG* 3.4 29.4 - - - +
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Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 5.0 1.3 - - - +
389B THR* 3.3 7.4 - - - +
390B VAL* 1.3 81.0 - - - +
392B LYS* 1.3 80.1 + - - +
394B THR* 5.7 0.9 - - - -
397B ASP* 3.7 32.1 - - - +
399B ASN* 2.6 37.6 + - - +
400B SER* 3.4 7.8 + - - +
401B ILE* 3.1 54.8 + - + +
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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