Contacts of the strand formed by residues 377 - 385 (chain B) in PDB entry 3THW
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 ILE 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B GLU* 3.2 40.6 - - + +
365B ASN 3.2 18.8 - - - +
366B LYS* 4.4 22.4 - - + +
367B GLU 5.7 2.9 - - - +
375B GLY 4.2 0.4 - - - +
376B ASN* 1.3 76.6 - - - +
378B PHE* 1.3 67.3 + - - +
379B ILE* 4.1 16.6 - - + -
397B GLN* 3.1 7.2 - - - +
398B ASP 2.7 36.8 + - - +
402B ARG* 3.4 36.8 - - - +
424B SER* 4.6 4.0 - - - +
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Residues in contact with PHE 378 (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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364B GLU* 3.5 0.7 - - - -
365B ASN* 3.0 55.8 + - - +
367B GLU 4.7 7.8 + - - +
368B ASN* 3.2 25.8 - - - +
377B ILE* 1.3 81.1 - - - +
379B ILE* 1.3 60.8 + - - +
395B SER* 4.1 13.2 - - - -
396B PHE* 3.2 36.1 - - - -
397B GLN* 3.3 23.1 - - + +
487B GLU* 3.6 29.4 - - - -
488B LYS* 5.1 0.4 - - + -
489B PRO* 3.5 27.7 - - + +
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Residues in contact with ILE 379 (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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362B ILE* 4.0 18.8 - - + -
363B SER 3.2 11.9 - - - +
364B GLU* 4.1 17.9 - - + +
377B ILE* 4.1 19.5 - - + +
378B PHE* 1.3 77.1 - - - +
380B GLY* 1.3 65.2 + - - +
381B ILE* 4.1 14.8 - - + -
395B SER* 3.3 3.1 - - - -
396B PHE* 2.6 50.7 + - + +
398B ASP* 4.5 11.7 - - + -
402B ARG* 4.6 6.1 - - - +
405B LEU* 4.0 35.0 - - + -
427B THR* 4.8 0.7 - - - +
489B PRO* 4.0 4.1 - - - +
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Residues in contact with GLY 380 (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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363B SER* 2.7 36.1 + - - +
379B ILE* 1.3 74.5 - - - +
381B ILE* 1.3 62.1 + - - -
394B ASP 3.5 6.7 - - - -
489B PRO* 3.7 19.2 - - - +
490B VAL* 4.0 10.1 - - - -
493B SER* 3.1 13.8 + - - -
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Residues in contact with ILE 381 (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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360B LEU* 3.7 20.4 - - + -
361B CYS 3.2 11.2 - - - +
362B ILE* 4.3 12.3 - - + -
379B ILE* 4.1 16.2 - - + -
380B GLY* 1.3 75.4 - - - +
382B VAL* 1.3 71.4 + - - +
383B GLY 5.1 0.7 - - - +
392B VAL* 5.3 2.9 - - + -
393B PHE* 3.3 2.0 - - - +
394B ASP* 2.8 52.2 + - + +
396B PHE* 4.3 10.8 - - + -
405B LEU* 4.4 9.4 - - + -
408B ARG* 3.8 27.8 - - + -
412B LEU* 5.2 2.9 - - + -
490B VAL* 4.8 1.2 - - - +
519B LEU* 4.0 19.1 - - + -
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Residues in contact with VAL 382 (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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360B LEU* 4.2 0.4 - - - -
361B CYS* 3.1 30.8 + - - +
381B ILE* 1.3 80.1 - - - +
383B GLY* 1.3 60.4 + - - +
384B VAL* 4.7 9.6 - - + -
391B VAL* 4.9 5.8 - - + -
392B VAL 3.4 9.2 - - - +
393B PHE* 4.4 11.0 - - + -
490B VAL* 3.4 28.7 - - - +
493B SER* 3.4 19.9 + - - +
494B LEU* 3.8 24.5 - - + +
497B ILE* 3.9 20.1 - - + +
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Residues in contact with GLY 383 (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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358B TYR* 4.6 4.0 - - - -
359B LEU 3.3 9.4 - - - -
360B LEU* 4.0 14.9 - - - +
381B ILE* 4.1 0.4 - - - +
382B VAL* 1.3 72.0 - - - +
384B VAL* 1.3 67.0 + - - +
390B GLU 4.0 0.2 - - - +
391B VAL 3.6 0.2 - - - -
392B VAL* 2.6 51.1 + - - +
412B LEU* 4.7 7.0 - - - -
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Residues in contact with VAL 384 (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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358B TYR* 4.1 4.4 - - - -
359B LEU* 2.9 61.7 + - + +
382B VAL* 4.7 4.3 - - + -
383B GLY* 1.3 80.9 - - - +
385B GLN* 1.3 59.8 + - - +
386B PRO* 3.6 5.6 - - + +
390B GLU 3.4 4.5 - - - -
391B VAL* 4.2 10.8 - - + -
497B ILE* 4.0 18.2 - - + -
501B LEU* 4.2 13.0 - - + -
509B MET* 3.5 21.3 - - + -
510B LEU* 4.1 19.5 - - + -
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Residues in contact with GLN 385 (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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350B ILE* 4.2 6.4 - - - +
356B THR* 3.3 19.1 - - - +
357B SER* 2.9 48.2 + - - +
358B TYR* 3.8 23.3 - - + -
384B VAL* 1.3 75.3 - - - +
386B PRO* 1.3 52.4 - - - +
387B ALA* 3.0 13.3 + - + +
388B THR* 3.1 28.6 + - - +
389B GLY* 2.7 33.8 + - - -
390B GLU* 3.0 27.3 + - - +
509B MET* 4.1 2.5 - - - -
565B ARG* 4.6 2.3 - - - +
569B LYS* 5.7 1.0 - - - +
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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