Contacts of the strand formed by residues 381 - 385 (chain X) in PDB entry 1T6B
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 381 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264X VAL* 3.7 22.1 - - + +
366X TYR* 4.5 2.9 + - - -
379X PRO 3.9 5.2 + - - -
380X THR* 1.3 82.1 - - - +
382X SER* 1.3 66.4 + - - +
383X LEU 3.8 0.5 + - - -
392X ALA 3.5 0.2 - - - +
393X THR* 3.3 4.3 - - - -
394X ILE* 2.7 47.5 + - - +
450X LEU* 4.0 14.6 - - + -
451X ASP 3.1 18.6 - - - +
452X THR* 3.0 30.3 + - - +
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Residues in contact with SER 382 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380X THR* 5.9 0.9 - - - +
381X THR* 1.3 75.1 - - - +
383X LEU* 1.4 60.7 + - - +
384X VAL* 3.6 18.3 + - - +
390X THR* 4.0 16.8 + - - +
392X ALA 3.2 6.1 - - - -
393X THR* 4.6 5.6 + - - +
449X ARG 3.7 0.2 - - - +
450X LEU* 3.4 5.2 - - - -
451X ASP* 2.9 37.9 + - - +
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Residues in contact with LEU 383 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266X MET* 4.2 9.4 - - + -
360X LEU* 4.1 20.9 - - + -
381X THR 3.8 1.6 + - - -
382X SER* 1.4 69.3 - - - +
384X VAL* 1.3 57.8 + - - +
390X THR* 3.5 4.5 - - - -
391X LEU* 2.7 43.1 + - + -
392X ALA* 2.7 31.1 + - + +
394X ILE* 4.6 4.2 - - + +
421X LEU* 3.8 29.4 - - + -
432X ILE* 4.7 1.8 - - + -
448X LEU* 3.9 26.9 - - + -
449X ARG 3.7 5.8 - - - +
450X LEU* 3.6 26.6 - - + +
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Residues in contact with VAL 384 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382X SER* 3.8 24.2 - - - +
383X LEU* 1.3 80.2 - - - +
385X LEU* 1.3 76.4 + - - +
386X GLY 4.1 1.5 + - - +
387X LYS 4.0 0.9 - - - +
388X ASN* 3.6 26.2 - - - +
389X GLN 3.7 6.5 - - - +
390X THR* 4.3 8.7 - - - +
391X LEU* 5.2 0.7 - - - -
448X LEU* 3.7 9.9 - - - +
449X ARG* 2.7 69.5 + - - +
451X ASP* 4.0 7.4 - - - +
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Residues in contact with LEU 385 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384X VAL* 1.3 71.2 - - - +
386X GLY* 1.3 73.0 + - - +
387X LYS 3.5 0.2 + - - -
388X ASN 3.6 0.2 + - - -
389X GLN* 3.1 61.1 + - - +
391X LEU* 4.3 18.1 - - + +
434X MET* 5.0 1.3 - - + -
438X GLN* 3.7 35.9 - - + +
441X GLU* 4.0 7.2 - - + +
442X LEU* 3.4 45.1 - - + +
445X THR* 5.0 3.1 - - - +
447X GLN 4.1 4.5 - - - +
448X LEU* 3.7 10.8 - - + -
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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