Contacts of the helix formed by residues 530 - 548 (chain L) in PDB entry 6PSS
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 LEU 530 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249I GLY 3.9 25.4 - - - +
1250I SER* 4.7 7.9 - - - -
1251I TYR* 4.8 7.2 - - + +
525L ASP 5.9 2.7 - - - +
528L LEU* 4.1 8.0 + - + +
529L GLU* 1.3 78.2 + - - +
531L PRO* 1.3 67.8 - - + +
532L LEU* 3.1 6.7 - - + +
533L ASP* 3.0 42.9 + - - +
534L SER* 3.1 9.4 + - - -
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Residues in contact with PRO 531 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248I THR* 3.7 30.5 - - + +
1251I TYR* 4.9 8.1 - - + +
1301I ARG* 4.8 6.5 - - - +
1302I THR* 3.7 28.7 - - + +
1305I TYR* 3.3 45.9 - - + +
1306I LYS* 5.5 0.5 - - - +
529L GLU 3.8 2.7 - - - +
530L LEU* 1.3 87.6 - - + +
532L LEU* 1.3 60.1 + - - +
534L SER* 3.9 6.5 - - - -
535L ALA* 3.3 16.3 + - - +
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Residues in contact with LEU 532 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305I TYR* 3.9 12.1 - - + +
378J LYS* 6.1 1.8 - - - -
382J TYR* 3.8 29.6 - - + +
394J ILE* 3.8 26.5 - - + +
395J LYS* 6.0 1.1 - - - -
398J LYS* 3.7 39.0 - - + -
530L LEU* 3.0 3.5 + - + -
531L PRO* 1.3 78.1 - - - +
533L ASP* 1.3 60.8 + - - +
535L ALA* 3.6 0.9 + - - -
536L THR* 2.3 41.3 + - - +
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Residues in contact with ASP 533 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395J LYS* 5.0 10.0 - - - +
398J LYS* 6.1 0.5 - - - -
529L GLU* 5.5 7.5 - - + +
530L LEU* 3.0 30.5 + - - +
532L LEU* 1.3 83.1 - - - +
534L SER* 1.3 58.5 + - - +
536L THR* 3.4 8.0 - - - -
537L THR* 2.7 34.2 + - - +
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Residues in contact with SER 534 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1302I THR* 4.8 9.0 - - - -
1306I LYS* 3.2 25.2 + - - -
529L GLU* 4.4 19.5 - - - +
530L LEU 3.1 13.8 + - - -
531L PRO* 3.9 9.6 - - - -
533L ASP* 1.3 78.3 - - - +
535L ALA* 1.3 52.8 + - - +
537L THR* 3.2 8.0 + - - -
538L GLU* 2.7 33.6 + - - +
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Residues in contact with ALA 535 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1305I TYR* 4.5 7.0 - - + +
1306I LYS* 4.0 22.8 - - + +
1309I VAL* 5.3 3.1 - - + -
394J ILE* 4.1 23.8 - - + +
531L PRO 3.3 17.4 + - - +
534L SER* 1.3 77.0 + - - +
536L THR* 1.3 60.8 + - - +
538L GLU* 3.7 9.6 - - - +
539L SER* 2.9 30.3 + - - -
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Residues in contact with THR 536 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394J ILE* 3.4 18.7 - - + +
395J LYS* 3.4 42.3 - - + +
532L LEU* 2.3 32.1 + - - +
533L ASP* 3.4 9.3 - - - -
534L SER 3.2 0.2 - - - -
535L ALA* 1.3 76.1 - - - +
537L THR* 1.3 57.8 + - - +
540L LEU* 2.9 27.2 + - + +
610L PHE* 3.2 31.2 - - + -
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Residues in contact with THR 537 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896I THR* 5.0 18.6 - - + +
898I GLU* 5.2 4.2 - - - +
533L ASP* 2.7 28.4 + - - +
534L SER* 3.5 8.2 - - - -
536L THR* 1.3 73.3 - - - +
538L GLU* 1.3 62.1 + - - +
540L LEU* 3.3 11.0 + - + +
541L ARG* 3.1 24.9 + - - +
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Residues in contact with GLU 538 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1306I LYS* 3.4 40.1 - - - +
1310I ASP* 4.8 14.9 - - - +
534L SER 2.7 20.7 + - - +
535L ALA* 4.0 7.3 - - - +
537L THR* 1.3 75.2 - - - +
539L SER* 1.3 66.1 + - - +
541L ARG* 3.2 30.3 + - + +
542L ALA* 3.4 8.0 + - - +
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Residues in contact with SER 539 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394J ILE* 5.2 7.4 - - - -
535L ALA 2.9 19.1 + - - -
536L THR* 4.8 0.4 - - - -
538L GLU* 1.3 80.1 + - - +
540L LEU* 1.3 60.5 + - - +
542L ALA* 3.4 6.7 + - - +
543L ALA* 2.9 29.8 + - - +
610L PHE* 3.4 17.5 - - - -
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Residues in contact with LEU 540 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898I GLU* 3.4 32.4 - - + +
899I GLU* 4.0 16.2 - - - +
902I LEU* 4.7 11.7 - - + -
536L THR* 2.9 20.2 + - + +
537L THR* 3.6 10.8 - - + +
538L GLU 3.2 0.4 - - - -
539L SER* 1.3 75.2 - - - +
541L ARG* 1.3 60.1 + - - +
543L ALA* 4.2 0.7 - - + -
544L THR* 3.0 30.5 + - - +
607L LEU* 4.1 17.3 - - + -
610L PHE* 3.3 41.2 - - + +
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Residues in contact with ARG 541 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898I GLU* 3.4 33.7 + - - +
537L THR* 3.1 16.3 + - - +
538L GLU* 3.3 21.0 - - + +
539L SER 3.2 0.2 - - - -
540L LEU* 1.3 79.0 - - - +
542L ALA* 1.3 59.1 + - - +
544L THR* 3.8 3.8 + - - +
545L HIS* 3.4 19.2 + - - +
566L ASP* 5.6 9.7 - - - +
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Residues in contact with ALA 542 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538L GLU* 3.4 7.7 + - - +
539L SER* 3.4 10.7 + - - +
541L ARG* 1.3 78.6 - - - +
543L ALA* 1.3 61.2 + - - +
544L THR 3.2 0.4 - - - -
545L HIS* 3.2 8.3 + - + +
546L ASP* 3.1 34.3 + - - +
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Residues in contact with ALA 543 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539L SER 2.9 18.4 + - - +
540L LEU 4.1 2.7 - - - +
542L ALA* 1.3 74.5 - - - +
544L THR* 1.3 63.2 + - - +
546L ASP* 3.7 5.1 + - - +
547L VAL* 3.3 24.9 + - - +
606L VAL* 4.2 20.1 - - + +
607L LEU* 3.9 9.8 - - + +
610L PHE* 3.6 26.9 - - + -
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Residues in contact with THR 544 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898I GLU* 3.6 33.5 + - + +
901I LEU* 3.9 19.5 - - + +
902I LEU* 5.9 0.7 - - - +
540L LEU* 3.0 19.2 + - - +
541L ARG 4.0 2.5 - - - +
543L ALA* 1.3 77.0 - - - +
545L HIS* 1.3 53.1 + - - +
546L ASP 3.1 0.2 - - - -
547L VAL* 3.1 6.5 + - - +
548L LEU* 2.7 57.5 + - + +
565L ILE* 4.3 7.0 - - + -
607L LEU* 4.4 12.6 - - - +
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Residues in contact with HIS 545 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541L ARG 3.4 13.4 + - - +
542L ALA* 3.2 14.2 + - + +
544L THR* 1.3 79.8 - - - +
546L ASP* 1.3 65.5 + - - +
548L LEU* 3.8 3.5 - - - -
549L ALA* 3.1 23.1 + - + +
560L ARG* 3.1 30.3 + - - +
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Residues in contact with ASP 546 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542L ALA* 3.1 18.3 + - - +
543L ALA* 4.2 6.3 - - - +
544L THR 3.1 0.2 - - - -
545L HIS* 1.3 85.1 - - - +
547L VAL* 1.3 65.0 + - - +
548L LEU 3.4 0.4 - - - -
549L ALA* 3.2 19.8 + - - +
550L GLY* 3.6 5.0 + - - -
606L VAL* 6.3 1.8 - - + -
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Residues in contact with VAL 547 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901I LEU* 5.9 2.2 - - + -
543L ALA 3.3 14.1 + - - +
544L THR* 3.1 5.9 + - - +
546L ASP* 1.3 78.9 - - + +
548L LEU* 1.3 59.9 + - + +
549L ALA 3.1 1.1 - - - -
550L GLY* 3.0 23.1 + - - -
551L LEU* 3.9 4.7 + - - +
598L LEU* 3.7 38.8 - - + +
603L ARG* 3.8 23.6 + - - +
606L VAL* 4.4 12.3 - - + -
607L LEU* 3.7 32.5 - - + -
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Residues in contact with LEU 548 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901I LEU* 4.3 12.8 - - + -
544L THR* 2.7 44.0 + - + +
545L HIS* 3.8 1.8 - - - +
547L VAL* 1.3 73.0 - - + +
549L ALA* 1.3 59.9 + - - +
550L GLY 3.2 1.3 - - - -
551L LEU* 3.7 35.7 + - + +
556L ALA* 4.0 20.7 - - + +
559L LEU* 4.6 10.8 - - + +
560L ARG* 3.5 52.0 + - + +
565L ILE* 4.1 11.2 - - + -
598L LEU* 4.9 5.8 - - + -
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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
------------------------------------------------------------
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