Contacts of the helix formed by residues 540 - 558 (chain A) in PDB entry 4OSI
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 GLY 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A ILE 3.4 12.9 + - - -
506A GLY 5.6 0.2 - - - -
538A ASN 3.6 0.4 + - - -
539A GLY* 1.3 73.5 - - - -
541A GLY* 1.3 66.8 + - - +
542A LYS 3.0 3.6 - - - -
543A GLN* 2.9 17.6 + - - +
544A ALA* 3.2 10.1 + - - +
10I A 3.6 39.8 - - - -
11I T 4.1 4.0 + - - +
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Residues in contact with GLY 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ILE 5.1 0.4 + - - -
506A GLY 5.3 1.0 + - - -
510A ALA* 4.3 8.9 - - - +
535A ILE 4.1 10.7 - - - +
536A ALA* 4.0 15.0 - - - -
538A ASN 3.3 17.1 + - - -
540A GLY* 1.3 75.8 - - - +
542A LYS* 1.3 62.9 + - - +
544A ALA* 3.0 5.9 + - - +
545A LEU* 2.9 32.8 + - - +
10I A 4.9 0.2 + - - -
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Residues in contact with LYS 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLN* 3.6 48.6 - - + +
510A ALA* 4.3 5.1 - - - +
512A GLU* 5.9 0.8 + - - +
513A THR* 2.9 28.0 + - - +
540A GLY* 2.9 1.4 + - - -
541A GLY* 1.3 75.8 - - - +
543A GLN* 1.3 75.4 + - - +
545A LEU* 3.6 7.0 - - - +
546A GLU* 2.9 50.3 + - - +
10I A 3.9 8.7 + - - +
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Residues in contact with GLN 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A GLY 2.9 4.8 + - - +
542A LYS* 1.3 93.3 - - - +
544A ALA* 1.3 55.0 + - - +
546A GLU* 3.4 9.7 + - - +
547A THR* 2.5 38.5 + - - -
576A LYS* 3.1 40.2 + - + +
10I A 3.1 58.1 + - - +
11I T 3.5 15.0 - - - +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ILE* 3.5 26.2 - - + +
540A GLY 3.2 6.5 + - - +
541A GLY* 3.0 9.9 + - - +
543A GLN* 1.3 76.3 - - - +
545A LEU* 1.3 68.0 + - - +
547A THR* 3.7 2.0 - - - -
548A VAL* 2.9 26.7 + - - +
570A ALA* 4.0 17.5 - - + +
572A HIS 5.2 2.2 - - - +
575A GLY* 4.7 4.3 - - - +
576A LYS* 4.2 17.4 - - - +
579A LEU* 4.5 0.4 - - - +
11I T 5.2 0.2 + - - -
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Residues in contact with LEU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ALA 4.0 3.1 - - - +
513A THR* 3.7 31.9 - - + -
514A VAL* 3.6 32.5 - - + +
517A LEU* 4.4 7.2 - - + -
521A LEU* 3.9 25.8 - - + +
532A VAL* 4.4 11.7 - - + +
535A ILE* 3.7 25.0 - - + +
536A ALA* 4.3 5.4 - - + -
541A GLY 2.9 24.5 + - - +
542A LYS* 3.6 2.9 - - - +
544A ALA* 1.3 73.7 - - - +
546A GLU* 1.3 57.3 + - - +
548A VAL* 2.9 21.4 + - + +
549A GLN* 2.9 15.4 + - - +
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Residues in contact with GLU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A THR* 4.1 14.1 + - + +
516A ARG* 3.8 17.5 + - - +
517A LEU* 4.2 12.3 - - + -
542A LYS* 2.9 53.0 + - - +
543A GLN* 4.0 10.5 - - - +
545A LEU* 1.3 75.9 - - - +
547A THR* 1.3 58.7 + - - +
549A GLN* 3.5 9.2 + - - +
550A ARG* 3.0 31.4 + - - +
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Residues in contact with THR 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A GLN 2.5 22.7 + - - -
544A ALA 3.7 3.1 - - - -
546A GLU* 1.3 76.6 - - - +
548A VAL* 1.3 59.1 + - - +
550A ARG* 3.8 18.4 + - - +
551A LEU* 2.9 42.8 + - + +
576A LYS* 2.8 47.7 - - + +
579A LEU* 3.8 18.7 - - + +
580A GLU* 4.1 10.1 - - + -
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Residues in contact with VAL 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A LEU* 4.2 15.9 - - + -
525A HIS* 4.7 0.2 - - - +
527A LEU* 4.2 9.2 - - + -
535A ILE* 4.5 13.0 - - + -
544A ALA 2.9 16.6 + - - +
545A LEU* 2.9 9.2 + - - +
547A THR* 1.3 76.0 - - - +
549A GLN* 1.3 62.8 + - - +
551A LEU 4.3 0.2 - - - +
552A LEU* 2.9 54.2 + - + +
566A VAL* 4.4 10.8 - - + -
567A VAL* 6.1 0.2 - - + -
570A ALA* 3.5 29.8 - - + -
579A LEU* 3.6 11.2 - - + -
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Residues in contact with GLN 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A ARG* 4.6 2.7 + - - +
517A LEU* 3.0 43.4 - - + +
520A VAL* 5.3 11.5 - - + +
521A LEU* 4.2 13.9 - - + +
525A HIS* 3.1 33.5 + - + +
545A LEU 2.9 11.3 + - - +
546A GLU* 3.7 11.9 + - - +
548A VAL* 1.3 78.0 - - - +
550A ARG* 1.3 66.9 + - - +
553A PRO* 3.9 5.5 - - - +
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Residues in contact with ARG 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A GLU 3.0 17.7 + - - +
547A THR* 4.1 21.5 + - - +
549A GLN* 1.3 84.0 - - - +
551A LEU* 1.3 90.3 + - + +
552A LEU 3.8 0.2 - - - -
553A PRO* 4.2 4.8 - - - +
554A VAL* 3.7 13.5 - - - +
576A LYS* 4.6 5.7 - - - +
580A GLU* 3.1 40.2 + - - -
583A GLN* 5.1 1.4 + - - -
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Residues in contact with LEU 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A THR* 2.9 26.6 + - + +
548A VAL* 5.0 0.4 - - - -
550A ARG* 1.3 118.1 - - - +
552A LEU* 1.3 61.2 + - - +
553A PRO* 3.4 2.5 - - - -
554A VAL* 4.2 13.6 - - + +
555A LEU* 2.9 44.8 + - + +
566A VAL* 5.6 0.2 - - - -
579A LEU* 4.1 16.8 - - + +
580A GLU* 4.7 2.0 - - - +
583A GLN* 3.3 48.9 - - + +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A HIS* 3.8 24.0 - - + +
527A LEU* 3.6 40.4 - - + -
548A VAL* 2.9 24.7 + - + +
551A LEU* 1.3 76.9 - - - +
553A PRO* 1.3 62.4 - - + +
555A LEU* 3.3 3.5 + - - +
556A CYS* 2.8 51.6 + - + +
563A PRO* 4.1 9.0 - - + +
566A VAL* 3.6 28.9 - - + +
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Residues in contact with PRO 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A HIS* 4.2 11.2 - - + +
549A GLN 3.9 16.2 - - - +
550A ARG 4.2 4.7 - - - +
551A LEU 3.5 2.7 - - - +
552A LEU* 1.3 93.4 - - + +
554A VAL* 1.3 70.5 + - + +
555A LEU 3.0 0.2 + - - -
556A CYS* 3.1 3.7 + - + -
557A GLN* 2.5 55.7 + - + +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A ARG 3.7 22.9 - - - +
551A LEU* 4.4 13.0 - - + +
552A LEU 3.5 0.2 - - - -
553A PRO* 1.3 80.0 - - + +
555A LEU* 1.3 59.2 + - - +
557A GLN* 4.5 5.4 - - - -
558A ALA* 3.0 26.7 + - + +
559A HIS* 3.2 27.4 + - + -
583A GLN* 4.6 13.2 - - + +
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 2.9 36.5 + - + +
552A LEU* 3.6 3.4 - - - +
554A VAL* 1.3 77.8 - - - +
556A CYS* 1.3 57.7 + - - +
559A HIS* 3.3 28.8 + - + +
560A GLY 3.1 22.5 + - - -
561A LEU* 3.4 28.9 + - + +
566A VAL* 4.1 18.6 - - + -
569A ILE* 5.4 0.9 - - + -
579A LEU* 3.9 30.3 - - + +
582A VAL* 4.5 5.4 - - + -
583A GLN* 3.8 30.1 - - + +
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Residues in contact with CYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A LEU* 2.8 47.2 + - + +
553A PRO* 3.9 3.6 - - + +
555A LEU* 1.3 70.2 - - - +
557A GLN* 1.3 66.3 + - + +
560A GLY* 3.3 15.4 - - - -
561A LEU 2.8 28.1 + - - +
562A THR 3.7 2.5 - - - -
563A PRO* 3.6 23.8 - - - -
566A VAL* 4.2 2.0 - - - -
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Residues in contact with GLN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A PRO* 2.5 37.7 + - + +
554A VAL* 4.4 3.1 - - - +
556A CYS* 1.3 77.2 - - + +
558A ALA* 1.3 62.3 + - + +
560A GLY* 4.3 1.2 + - - -
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Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A VAL* 3.0 19.4 + - + +
557A GLN* 1.3 78.6 - - + +
559A HIS* 1.3 71.5 + - + +
560A GLY* 2.9 11.3 + - - -
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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