Contacts of the helix formed by residues 377 - 388 (chain J) in PDB entry 6PSU
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 PHE 377 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J LEU* 4.7 12.8 - - + -
373J ALA 3.2 21.6 + - - +
374J LEU 4.4 3.4 - - - -
375J GLU 3.3 0.6 - - - -
376J LEU* 1.3 81.4 - - + +
378J LYS* 1.3 64.8 + - - +
379J PRO* 3.5 1.6 - - - -
380J PHE* 3.5 30.2 + + + -
381J ILE* 3.1 26.1 + - + +
412J LEU* 5.7 0.2 - - + -
415J VAL* 4.8 6.5 - - + -
416J ILE* 3.3 35.4 - - + -
419J HIS* 3.5 22.0 - + - -
421J VAL* 3.6 31.6 - - + -
439J PRO* 5.1 0.2 - - + -
470J VAL* 3.5 30.7 - - + -
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Residues in contact with LYS 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247I SER* 3.9 11.9 - - - +
1305I TYR* 5.8 0.4 - - - +
374J LEU* 3.9 25.6 + - + +
375J GLU* 3.1 44.6 + - - +
377J PHE* 1.3 75.8 - - - +
379J PRO* 1.3 74.3 - - + +
381J ILE* 2.9 16.4 + - - +
382J TYR* 2.9 54.1 + - + +
398J LYS* 5.1 5.2 - - - -
401J VAL* 4.7 10.3 - - + +
402J GLU* 6.2 1.4 - - - +
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Residues in contact with PRO 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247I SER* 3.9 10.5 - - - +
1305I TYR* 3.3 39.3 - - + +
1308I ILE* 3.3 27.4 - - + +
1309I VAL* 4.1 5.8 - - + +
349J TYR* 3.8 16.4 - - + +
376J LEU 4.0 5.8 - - - +
377J PHE 3.7 1.3 - - - -
378J LYS* 1.3 95.0 - - + +
380J PHE* 1.3 64.9 + - + +
382J TYR* 3.3 14.3 + - + +
383J GLY* 2.9 19.8 + - - -
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Residues in contact with PHE 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308I ILE* 3.4 33.6 - - + +
1313I HIS* 3.3 33.2 - + - -
349J TYR* 6.0 0.7 - + - -
376J LEU 4.7 3.8 - - - -
377J PHE* 3.6 39.5 - + + +
378J LYS 3.2 0.6 - - - -
379J PRO* 1.3 81.5 - - + +
381J ILE* 1.3 57.5 + - - +
383J GLY* 3.1 2.6 + - - -
384J LYS* 2.9 32.5 + - + +
415J VAL* 4.6 16.2 - - + -
419J HIS* 3.5 32.5 - + - -
470J VAL* 4.3 4.5 - - + -
472J LEU* 4.0 24.0 - - + -
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Residues in contact with ILE 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J LEU* 4.5 13.5 - - + +
377J PHE* 3.1 14.5 + - + +
378J LYS* 2.9 10.1 + - + +
380J PHE* 1.3 76.2 - - - +
382J TYR* 1.3 61.7 + - + +
384J LYS* 3.3 1.8 + - - +
385J LEU* 2.9 33.4 + - + +
401J VAL* 3.8 27.6 - - + -
408J VAL* 4.4 9.9 - - + +
411J ILE* 4.2 23.8 - - + -
412J LEU* 3.4 48.2 - - + -
415J VAL* 4.4 8.5 - - + -
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Residues in contact with TYR 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305I TYR* 3.3 28.0 - + - -
1309I VAL* 4.7 7.9 - - + -
378J LYS* 2.9 59.7 + - + +
379J PRO* 3.5 9.4 - - + +
381J ILE* 1.3 78.8 - - + +
383J GLY* 1.3 63.2 + - - +
385J LEU* 3.2 2.5 + - - +
386J GLU* 3.0 29.5 + - - +
394J ILE* 4.5 16.4 - - + -
397J ALA* 4.3 22.3 - - + +
398J LYS* 3.2 27.1 - - + +
401J VAL* 3.5 29.8 - - + +
532L LEU* 3.4 17.6 - - + +
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Residues in contact with GLY 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308I ILE 4.6 2.7 - - - -
1309I VAL* 3.4 30.5 - - - +
1311I GLY 5.7 0.4 - - - -
379J PRO 2.9 14.6 + - - -
380J PHE 3.1 3.8 + - - -
382J TYR* 1.3 76.9 - - - +
384J LYS* 1.3 59.7 + - - +
386J GLU* 3.4 4.2 + - - +
387J LEU* 2.9 28.1 + - - +
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Residues in contact with LYS 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380J PHE* 2.9 15.1 + - + +
383J GLY* 1.3 77.0 - - - +
385J LEU* 1.3 60.3 + - - +
387J LEU* 3.1 26.6 + - + +
388J ARG* 2.9 68.2 + - - +
411J ILE* 3.4 23.2 + - + +
414J GLU* 4.5 9.3 + - - +
415J VAL* 3.2 33.1 - - + +
45K LYS* 4.9 12.3 - - - +
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Residues in contact with LEU 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381J ILE* 2.9 19.6 + - + +
382J TYR* 3.9 4.7 - - - +
384J LYS* 1.3 77.0 - - - +
386J GLU* 1.3 60.8 + - - +
388J ARG* 4.0 1.1 - - - +
389J GLY 3.4 0.5 + - - -
390J LEU* 3.2 56.4 + - + -
391J ALA* 3.3 10.7 + - + -
397J ALA* 4.7 10.1 - - + +
400J MET* 3.3 30.3 - - + -
401J VAL* 4.0 14.8 - - + -
407J VAL* 4.8 4.3 - - + -
408J VAL* 3.9 19.3 - - + -
411J ILE* 3.7 29.6 - - + -
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Residues in contact with GLU 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309I VAL* 4.7 12.7 - - - +
1310I ASP* 5.5 0.9 - - - +
382J TYR 3.0 18.0 + - - +
383J GLY* 3.9 4.0 - - - +
385J LEU* 1.3 78.7 - - - +
387J LEU* 1.3 64.0 + - - +
388J ARG 3.2 0.4 - - - -
389J GLY* 3.3 11.0 + - - +
391J ALA* 5.1 4.7 - - + +
392J THR 4.7 9.9 - - - +
393J THR* 2.9 13.4 - - - +
394J ILE* 2.6 54.5 + - - +
397J ALA* 4.9 3.8 - - + -
539L SER* 6.1 1.4 - - - -
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Residues in contact with LEU 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383J GLY 2.9 18.0 + - - +
384J LYS* 3.1 28.9 + - + +
386J GLU* 1.3 77.7 - - - +
388J ARG* 1.3 65.9 + - + +
389J GLY 3.6 0.2 + - - -
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Residues in contact with ARG 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384J LYS* 2.9 44.4 + - - +
385J LEU* 4.3 1.3 - - - +
386J GLU 3.2 0.2 - - - -
387J LEU* 1.3 82.7 - - - +
389J GLY* 1.3 61.4 + - - +
390J LEU* 3.3 33.0 + - + +
411J ILE* 3.2 33.2 - - + +
414J GLU* 2.5 39.4 + - - -
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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